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Created on: 21-Dec-2010   Last updated on: 11-June-2011 |  How to cite this?
Total resources - 266
A compilation of SNP analysis resources
Dilna J.P, Kanika Mathuria, Krishna Azmeera and Mansi Gandhi (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
Haploview
www.broad.mit.edu/mpg/haploview/
1) Provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data. 2) Uses genotypic file (.ped file & .info file) as input and performs LD plots for highly associated markers and other statistics for it; also provides haplotype blocks for highly associated markers and performs other complex statistics for it (association tests for the SNP markers). 3) Mainly a useful tool for visualizing Hapmap data.
Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics. 2005 Jan 15;21(2):263-5. Epub 2004 Aug 5. PubMed PMID: 15297300.
2005
25
Freely downloadable
dbSNP
http://www.ncbi.nlm.nih.gov/projects/SNP/
A central repository for both single base nucleotide subsitutions and short deletion and insertion polymorphisms.
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11. PubMed PMID: 11125122.
2001
44
Online
HapMap
http://hapmap.ncbi.nlm.nih.gov/
Identifies and catalogs genetic similarities and differences in human beings and compares the genetic sequences of different individuals to find chromosomal regions where genetic variants are shared
International HapMap Consortium. The International HapMap Project. Nature. 2003 Dec 18;426(6968):789-96. PubMed PMID: 14685227.
2003
49
Online
1000 Genomes
http://www.1000genomes.org
1) Provides information on the validated haplotype map of 38 million single nucleotide polymorphisms, 1.4 million short insertions and deletions, and more than 14,000 larger deletions. 2) It aims to provide an accurate and better localization of disease associated variants in GWAS.
1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov 1;491(7422):56-65. doi: 10.1038/nature11632. PubMed PMID: 23128226; PubMed Central PMCID: PMC3498066
2012
51
PolyPhen
http://genetics.bwh.harvard.edu/pph/
Predicts the impact of an amino acid substitution on the structure and function of a human protein.
Ramensky V, Bork P, Sunyaev S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 2002 Sep 1;30(17):3894-900. PubMed PMID: 12202775.
2002
70
Online
WormBase
http://www.wormbase.org/
Contains over 10,000 alleles with molecular information, which facilitates the structure/function studies and sequencing data in the polymorphic strains, has identified over 1,70,000 single nucleotide polymorphisms.
Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, Fernandes J, Han M, Kishore R, Lee R, Müller HM, Nakamura C, Ozersky P, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW. WormBase: a comprehensive resource for nematode research. Nucleic Acids Res. 2010 Jan;38(Database issue):D463-7. Epub 2009 Nov 12. PubMed PMID: 19910365
2010
76
Online
SIFT - Sorting Tolerant From Intolerant
http://sift.jcvi.org/
1) Restrict to coding variants -input- chromosome coordinates, orientation (1,-1) and alleles divides the variants into coding & non-coding variants. 2) SIFT nonsynonymous single nucleotide variants (genome-scale)-input-chromosome coordinates, orientation (1,-1) and alleles shows where in genome region(genic & non genic region) they are present & also OMIM ID associated with that variant. 3) Classify coding indels (Insertion / Deletion polymorphisms)-input-chromosome coordinates, orientation (1,-1) and indels- filters them out to coding indels. 4)SIFT dbSNP-input- list of rs-ids having impact on protein function or not (tolerating/damaging) from NCBI's dbSNP (build 132) database.
Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 2003 Jul 1;31(13):3812-4. PubMed PMID: 12824425.
2003
87
URL not working (as on 30 Nov 2013)
HAP
1. http://www.hgmp.mrc.ac.uk/~jzhao 2. http://www.iop.kcl.ac.uk/IoP/Departments/PsychMed/GEpiBSt/software.shtml
Zhao JH. 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics. 2004 May 22;20(8):1325-6. Epub 2004 Feb 10. PubMed PMID: 14871868.
2004
92
1st URL is not working (as on 30 Nov 2013)
HMDB - Human Metabolome Database
http://www.hmdb.ca/
1) Contains detailed information about small molecule metabolites found in the human body. 2) The SNP data field (found in HMDB's Enzyme section) is displayed in the form of hyperlinked summary tables, which contains information on their type (synonymous, nonsynonymous), location, validation status and population distributions.
Wishart DS, Tzur D, Knox C, Eisner R, Guo AC, Young N, Cheng D, Jewell K, Arndt D, Sawhney S, Fung C, Nikolai L, Lewis M, Coutouly MA, Forsythe I, Tang P, Shrivastava S, Jeroncic K, Stothard P, Amegbey G, Block D, Hau DD, Wagner J, Miniaci J, Clements M, Gebremedhin M, Guo N, Zhang Y, Duggan GE, Macinnis GD, Weljie AM, Dowlatabadi R, Bamforth F, Clive D, Greiner R, Li L, Marrie T, Sykes BD, Vogel HJ, Querengesser L. HMDB: the Human Metabolome Database. Nucleic Acids Res. 2007 Jan;35(Database issue):D521-6. PubMed PMID: 17202168.
2007
92
Online
BioMart
http://www.biomart.org/
Applicable in solving biological use cases such as SNP selection for candidate gene screening or annotation of microarray results.
Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A. BioMart--biological queries made easy. BMC Genomics. 2009 Jan 14;10:22. PubMed PMID: 19144180.
2009
93
Online
GOLD - Graphical Overview of Linkage Disequilibrium
http://www.well.ox.ac.uk/asthma/GOLD
Abecasis GR, Cookson WO. GOLD--graphical overview of linkage disequilibrium. Bioinformatics. 2000 Feb;16(2):182-3. PubMed PMID: 10842743.
2000
95
URL not working (as on 30 Nov 2013)
PMUT
http://mmb2.pcb.ub.es:8080/PMut/
Provides fast and accurate prediction of single point amino acid mutations (which have a pathological character) by the use of neural networks.
Ferrer-Costa C, Gelpí JL, Zamakola L, Parraga I, de la Cruz X, Orozco M. PMUT: a web-based tool for the annotation of pathological mutations on proteins. Bioinformatics. 2005 Jul 15;21(14):3176-8. Epub 2005 May 6. PubMed PMID: 15879453.
2005
95
Online
SNPSpD - SNP SPectral Decomposition
http://gump.qimr.edu.au/general/daleN/SNPSpD/
Based on spectral decomposition, it provides a correlation between SNPs and linkage disequilibrium..
Nyholt DR. A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other. Am J Hum Genet. 2004 Apr;74(4):765-9. Epub 2004 Mar 2. PubMed PMID: 14997420.
2004
95
Online
JSNP - Japanese Single Nucleotide Polymorphisms
http://snp.ims.u-tokyo.ac.jp/
Detailed information on the variations in the Japanese population
Hirakawa M, Tanaka T, Hashimoto Y, Kuroda M, Takagi T, Nakamura Y. JSNP: a database of common gene variations in the Japanese population. Nucleic Acids Res. 2002 Jan 1;30(1):158-62. PubMed PMID: 11752280.
2002
95
Online
SNPper
http://snpper.chip.org/
Retrieves known human SNPs by position or by association with a gene.
Manske HM, Kwiatkowski DP. SNP-o-matic. Bioinformatics. 2009 Sep 15;25(18):2434-5. Epub 2009 Jul 2. PubMed PMID: 19574284.
2009
95
Online registration
ARTS
http://andromeda.gsf.de/arts
An advanced tool for retrieval of SNPs in mouse.
Klaften M, Hrabé de Angelis M. ARTS: a web-based tool for the set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W496-500. PubMed PMID: 15980520.
2005
96
Online (URL not working as on 26 October 2013)
DnaSP
http://www.ub.edu/dnasp
1) Analysis on multiple data files. 2) Haplotype phasing. 3) Analysis of insertion/deletion polymorphism data. 4) Visualizes sliding window results integration with available genome annotations in the UCSC browser.
Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics. 2009 Jun 1;25(11):1451-2. Epub 2009 Apr 3. PubMed PMID: 19346325.
2009
96
Freely downloadable
SNPs3D
http://www.snps3d.org/
Asssigns functional effects of non-synonymous SNPs based on structure and sequence analysis.
Yue P, Melamud E, Moult J. SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics. 2006 Mar 22;7:166. PubMed PMID: 16551372.
2006
96
Online
Structure
http://pritch.bsd.uchicago.edu/structure.html
A software package, which is used to investigate population structure. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
Not available
Not available
96
Freely downloadable
The SNP Consortium website
http://snp.cshl.org
Thorisson GA, Stein LD. The SNP Consortium website: past, present and future. Nucleic Acids Res. 2003 Jan 1;31(1):124-7. PubMed PMID: 12519964.
2003
96
Online
ECR browser
http://ecrbrowser.dcode.org/
Visualizes and analyzes Evolutionary Conserved Regions (ECRs) in genomes of sequenced species and provides annotation of different genomic features, such as known genes, gene predictions, repetitive elements and single nucleotide polymorphisms.
Ovcharenko I, Nobrega MA, Loots GG, Stubbs L. ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W280-6. PubMed PMID: 15215395.
2004
97
Online
PupaSuite
http://pupasuite.bioinfo.cipf.es/
Provides information on SNPs within a gene along with additional data for the SNP like- validation status, type, frequency/population data and putative functional properties (pathological SNPs, SNPs disrupting potential transcription factor binding sites, intron/exon boundaries), information about LD parameters (based on genotype data from HapMap) and identifies haplotype blocks and tag SNPs.
Conde L, Vaquerizas JM, Dopazo H, Arbiza L, Reumers J, Rousseau F, Schymkowitz J, Dopazo J. PupaSuite: finding functional single nucleotide polymorphisms for large-scale genotyping purposes. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W621-5. PubMed PMID: 16845085.
2006
97
Online registration
SLOPE
http://www-genepi.med.utah.edu/suppl/SLOPE/index.html
A fast and accurate tool for detecting structural variants like translocations and indels from targeted short-DNA reads.
Abel HJ, Duncavage EJ, Becker N, Armstrong JR, Magrini VJ, Pfeifer JD. SLOPE: a quick and accurate method for locating non-SNP structural variation from targeted next-generation sequence data. Bioinformatics. 2010 Nov 1;26(21):2684-8. Epub 2010 Sep 27. PubMed PMID: 20876606.
2010
97
Freely downloadable
SOAP2 (Short Oligonucleotide Analysis Package)
http://soap.genomics.org.cn/
Provides a feature of SNP detection from alignment of short reads on a reference genome.
Li R, Yu C, Li Y, Lam TW, Yiu SM, Kristiansen K, Wang J. SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics. 2009 Aug 1;25(15):1966-7. Epub 2009 Jun 3. PubMed PMID: 19497933.
2009
97
Freely downloadable
FASTSNP- Function analysis and selection tool for single nucleotide polymorphisms
http://fastsnp.ibms.sinica.edu.tw/pages/input_CandidateGeneSearch.jsp
Identifies and prioritizes high-risk SNPs according to their phenotypic risks and putative functional effects. A unique feature is that the functional effect information used for SNP prioritization is extracted from 11 external web servers at query time using a team of web wrapper agents, which keeps the data up-to- date.
Yuan HY, Chiou JJ, Tseng WH, Liu CH, Liu CK, Lin YJ, Wang HH, Yao A, Chen YT, Hsu CN. FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W635-41. PubMed PMID: 16845089.
2006
98
Online
Forage
http://biobase.biotech.kth.se/forage/
Unneberg P, Stromberg M, Sterky F. SNP discovery using advanced algorithms and neural networks. Bioinformatics. 2005 May 15;21(10):2528-30. Epub 2005 Mar 3. PubMed PMID: 15746291.
2005
98
URL not working (as on 30 Nov 2013)
GenoA - Genome Analyzer
NOT AVAILABLE
A data mining and visualization tool, which extracts exons and SNPs from mammalian genomic sequences.
Liu Y, Wang Y, Folander K, Xie G, Blevins R. An interactive tool for extracting exons and SNP from genomic sequence: isolation of HCN1 and HCN3 ion channel genes. J Bioinform Comput Biol. 2003 Oct;1(3):433-46. PubMed PMID: 15290763.
2003
98
-
MAGIC
http://cogent.iop.kcl.ac.uk/ MaGIC.cogx
Simpson CL, Hansen VK, Sham PC, Collins A, Powell JF, Al-Chalabi A. MaGIC: a program to generate targeted marker sets for genome-wide association studies. Biotechniques. 2004 Dec;37(6):996-9. PMID:15597550
2004
98
Freely downloadable [ URL not working (as on 30 Nov 2013)]
SEAN
http://http//zebrafish.doc.ic.ac.uk/Sean
Predicts SNPs by using multiple sequence alignment, which are produced from EST clusters.
Huntley D, Baldo A, Johri S, Sergot M. SEAN: SNP prediction and display program utilizing EST sequence clusters. Bioinformatics. 2006 Feb 15;22(4):495-6. Epub 2005 Dec 15. PubMed PMID: 16357032.
2006
98
URL not working (as on 30 Nov 2013)
SNP500Cancer
http://variantgps.nci.nih.gov/cgfseq/pages/snp500.do
Finds known or novel SNPs within genes, which are involved in cancer.
Packer BR, Yeager M, Burdett L, Welch R, Beerman M, Qi L, Sicotte H, Staats B, Acharya M, Crenshaw A, Eckert A, Puri V, Gerhard DS, Chanock SJ. SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D617-21. PubMed PMID: 16381944.
2006
98
Online
SNPStats
http://bioinfo.iconcologia.net/snpstats/start.htm
Performs analysis of multiple SNPs: haplotype frequency estimation, analysis of association of haplotypes with the response, including analysis of interactions.
Sole X, Guino E, Valls J, Iniesta R, Moreno V. SNPStats: a web tool for the analysis of association studies. Bioinformatics. 2006 Aug 1;22(15):1928-9. Epub 2006 May 23. PubMed PMID: 16720584.
2006
98
Online
ALFRED
http://alfred.med.yale.edu/alfred/index.asp
A compilation of allele frequencies for DNA sequence polymorphisms in anthropologically defined human populations.
Rajeevan H, Osier MV, Cheung KH, Deng H, Druskin L, Heinzen R, Kidd JR, Stein S, Pakstis AJ, Tosches NP, Yeh CC, Miller PL, Kidd KK. ALFRED: the ALelle FREquency Database. Update. Nucleic Acids Res. 2003 Jan 1;31(1):270-1. PubMed PMID: 12519999.
2003
98
Online
Panzea
http://www.panzea.org/
Finds polymorphism between two inbred lines of maize.
Zhao W, Canaran P, Jurkuta R, Fulton T, Glaubitz J, Buckler E, Doebley J, Gaut B, Goodman M, Holland J, Kresovich S, McMullen M, Stein L, Ware D. Panzea: a database and resource for molecular and functional diversity in the maize genome. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D752-7. PubMed PMID: 16381974.
2006
98
Online
Ecgene
http://genome.ewha.ac.kr/ECgene/
Predicts the transcript structure, expression and functions in context to alternative splicing and annotates the association of SNP and alternative splicing.
Lee Y, Lee Y, Kim B, Shin Y, Nam S, Kim P, Kim N, Chung WH, Kim J, Lee S. ECgene: an alternative splicing database update. Nucleic Acids Res. 2007 Jan;35(Database issue):D99-103. Epub 2006 Nov 28. PubMed PMID: 17132829.
2007
99
Online
IGG3
http://bioinfo.hku.hk/iggweb
Integrates large genotype datasets across genome-wide association studies and HapMap project for whole-genome imputation and individual-level meta-analysis.
Li MX, Jiang L, Kao PY, Sham PC, Song YQ. IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis. Bioinformatics. 2009 Jun 1;25(11):1449-50. Epub 2009 Apr 3. PubMed PMID: 19346322.
2009
99
Freely downloadable
LocusZoom
http://csg.sph.umich.edu/locuszoom/
Plots regional association results from genome-wide association scans or candidate gene studies.
Pruim RJ, Welch RP, Sanna S, Teslovich TM, Chines PS, Gliedt TP, Boehnke M, Abecasis GR, Willer CJ. LocusZoom: regional visualization of genome-wide association scan results. Bioinformatics. 2010 Sep 15;26(18):2336-7. Epub 2010 Jul 15. PMID:20634204
2010
99
Online
LS-SNP
http://modbase.compbio.ucsf.edu/LS-SNP/
It annotates nsSNPs and is useful in identifying candidate functional SNPs within a gene, haplotype or pathway and in probing molecular mechanisms responsible for functional impacts of nsSNPs.
Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, Haussler D, Sali A. LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. Bioinformatics. 2005 Jun 15;21(12):2814-20. Epub 2005 Apr 12. PubMed PMID: 15827081
2009
99
Online
Oryza SNP
http://www.oryzasnp.org/
Provides detailed information on the genetic variation present within and between diverse rice cultivars and landraces.
McNally KL, Bruskiewich R, Mackill D, Buell CR, Leach JE, Leung H. Sequencing multiple and diverse rice varieties. Connecting whole-genome variation with phenotypes. Plant Physiol. 2006 May;141(1):26-31. PubMed PMID: 16684934.
2006
99
Online
PANTHER Coding SNP Analysis Tool
http://www.pantherdb.org/tools/csnpScoreForm.jsp
Calculates the functional impact of a particular nonsynonymous (amino-acid changing) coding SNP on the protein. It estimates the subPSEC (substitution position-specific evolutionary conservation) score based on an alignment of evolutionarily related proteins.
Not available
Not available
99
Online
PEAS- Package for Elementary Analysis of SNP data
http://www.picb.ac.cn/~xushua/index.files/Download_PEAS.htm
A software package to facilitate the analyses of large data sets of single nucleotide polymorphisms (SNPs) for population genetics and molecular phylogenetics studies.
Xu S, Gupta S, Jin L. PEAS V1.0: a package for elementary analysis of SNP data. Mol Ecol Resour. 2010 Nov;10(6):1085-8. doi: 10.1111/j.1755-0998.2010.02862.x. PubMed PMID: 21565121.
2010
99
-
Quake
http://www.cbcb.umd.edu/software/quake
A program to detect and correct errors in DNA sequencing reads and helps users to demonstrate significant improvements in de novo assembly and SNP detection.
Kelley DR, Schatz MC, Salzberg SL. Quake: quality-aware detection and correction of sequencing errors. Genome Biol. 2010;11(11):R116. Epub 2010 Nov 29. PubMed PMID: 21114842.
2010
99
Freely downloadable
SNPeffect v2.0
http://snpeffect.vib.be/
A database for phenotyping human single nucleotide polymorphisms (SNPs) and mainly focuses on the molecular characterization and annotation of disease and polymorphism variants in the human proteome.
Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F. SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics. 2006 Sep 1;22(17):2183-5. Epub 2006 Jun 29. PubMed PMID: 16809394.
2006
99
URL not working (as on 30 Nov 2013)
WGAViewer
http://people.chgv.lsrc.duke.edu/~dg48//WGAViewer/
Ge D, Zhang K, Need AC, Martin O, Fellay J, Urban TJ, Telenti A, Goldstein DB. WGAViewer: software for genomic annotation of whole genome association studies. Genome Res. 2008 Apr;18(4):640-3. Epub 2008 Feb 6. PubMed PMID: 18256235.
2008
99
Freely downloadable. URL not working (as on 7 Nov 2013).
WHAP
http://pngu.mgh.harvard.edu/~purcell/whap/
Provides analysis of SNP haplotype associations with qualitative and quantitative traits in samples of individuals with or without parental genotype data.
Purcell S, Daly MJ, Sham PC. WHAP: haplotype-based association analysis. Bioinformatics. 2007 Jan 15;23(2):255-6. Epub 2006 Nov 21. PubMed PMID: 17118959.
2007
99
Freely downloadable
F-SNP
http://compbio.cs.queensu.ca/F-SNP/
Provides integrated information about the functional effects of SNPs mainly in terms of disease association studies.
Lee PH, Shatkay H. F-SNP: computationally predicted functional SNPs for disease association studies. Nucleic Acids Res. 2008 Jan;36(Database issue):D820-4. Epub 2007 Nov 5. PubMed PMID: 17986460.
2008
99
Online
HGVbase - Human Genome Variation Database
http://hgvbase.cgb.ki.se/
Important curated repository of nucleotide polymorphisms in humans with a goal to facilitate genotype-phenotype association analyses.
Fredman D, Siegfried M, Yuan YP, Bork P, Lehväslaiho H, Brookes AJ. HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources. Nucleic Acids Res. 2002 Jan 1;30(1):387-91. PubMed PMID: 11752345.
2002
99
Online
MODBASE
http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
A relational database of annotated comparative protein structure models and also provides information on single nucleotide polymorphisms.
Pieper U, Eswar N, Webb BM, Eramian D, Kelly L, Barkan DT, Carter H, Mankoo P, Karchin R, Marti-Renom MA, Davis FP, Sali A. MODBASE, a database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 2009 Jan;37(Database issue):D347-54. Epub 2008 Oct 23. PubMed PMID: 18948282.
2009
99
Online
MutDB
http://mutdb.org/
Annotates human variation data with protein structural and other functionally relevant information.
Singh A, Olowoyeye A, Baenziger PH, Dantzer J, Kann MG, Radivojac P, Heiland R, Mooney SD. MutDB: update on development of tools for the biochemical analysis of genetic variation. Nucleic Acids Res. 2008 Jan;36(Database issue):D815-9. Epub 2007 Sep 7. PubMed PMID: 17827212.
2008
99
Online
Rice DNA polymorphism database
http://shenghuan.shnu.edu.cn/ricemarker
Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN. Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiol. 2004 Jul;135(3):1198-205. PubMed PMID: 15266053.
2004
99
URL not working (as on 30 Nov 2013)
SNP resource for Rice
http://www.plantgenome.uga.edu/snp
Information on SNPs of Rice subspecies indica and japonica
Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH. An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. Genome Res. 2004 Sep;14(9):1812-9. PubMed PMID: 15342564.
2004
99
URL not working (as on 13 Sep 2013)
SNPeffect
http://snpeffect.vib.be/
Focuses on the annotation of disease and polymorphism variants present in the human proteome.
Reumers J, Maurer-Stroh S, Schymkowitz J, Rousseau F. SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non-synonymous SNPs. Bioinformatics. 2006 Sep 1;22(17):2183-5. Epub 2006 Jun 29. PubMed PMID: 16809394.
2006
99
Online
ToxoDB
http://toxodb.org/toxo/
Gajria B, Bahl A, Brestelli J, Dommer J, Fischer S, Gao X, Heiges M, Iodice J, Kissinger JC, Mackey AJ, Pinney DF, Roos DS, Stoeckert CJ Jr, Wang H, Brunk BP. ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Res. 2008 Jan;36(Database issue):D553-6. Epub 2007 Nov 14. PubMed PMID: 18003657.
2008
99
Online. Site opens in Mozilla but is not accessible through IE (as on 7 Oct 2013)
ALOHOMORA
http://gmc.mdc-berlin.de/alohomora/
Performs genome-wide linkage studies with high-density single nucleotide polymorphism (SNP) marker panels like the Affymetrix GeneChip Human Mapping 10K Array.
Ruschendorf F, Nurnberg P. ALOHOMORA: a tool for linkage analysis using 10K SNP array data. Bioinformatics. 2005 May 1;21(9):2123-5. Epub 2005 Jan 12. PubMed PMID: 15647291.
2005
100
Freely downloadable
2LD
http://www.hgmp.mrc.ac.uk/~jzhao
Zhao JH. 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics. 2004 May 22;20(8):1325-6. Epub 2004 Feb 10. PubMed PMID: 14871868.
2004
100
URL not working (as on 30 Nov 2013)
2SNP
http://alla.cs.gsu.edu/~software/2SNP/
1) Explores disease susceptibility prediction on genotype/haplotype data. 2) Provides phasing method based on 2-SNP haplotypes and also assists in tag selection.
Brinza D, Zelikovsky A. 2SNP: scalable phasing method for trios and unrelated individuals. IEEE/ACM Trans Comput Biol Bioinform. 2008 Apr-Jun;5(2):313-8. PubMed PMID: 18451440.
2008
100
Freely downloadable
ACCUSA
ftp://bbc.mdc-berlin.de/software
It considers both the read qualities as well as the reference genome's quality for detecting SNPs in the sequenced genome.
Frohler S, Dieterich C. ACCUSA--accurate SNP calling on draft genomes. Bioinformatics. 2010 May 15;26(10):1364-5. Epub 2010 Apr 1. PubMed PMID: 20363730.
2010
100
Freely downloadable
AssociationViewer
http://sourceforge.net/projects/associationview/
A Java application to display SNPs in a genomic context.
Martin O, Valsesia A, Telenti A, Xenarios I, Stevenson BJ. AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context. Bioinformatics. 2009 Mar 1;25(5):662-3. Epub 2009 Jan 25. PubMed PMID: 19168913
2009
100
Freely downloadable
AtPID
http://atpid.biosino.org/
Annotates Arabidopsis thaliana proteome along with information on the SNP phenotype.
Cui J, Li P, Li G, Xu F, Zhao C, Li Y, Yang Z, Wang G, Yu Q, Li Y, Shi T. AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res. 2008 Jan;36(Database issue):D999-1008. Epub 2007 Oct 25. PubMed PMID: 17962307.
2008
100
URL not working (as on 30 Nov 2013)
AutoSNPa
http://dna.leeds.ac.uk/autosnpa/
Visual analysis of SNP data and identification of autozygous chromosomal regions.
Carr IM, Flintoff KJ, Taylor GR, Markham AF, Bonthron DT. Interactive visual analysis of SNP data for rapid autozygosity mapping in consanguineous families. Hum Mutat. 2006 Oct;27(10):1041-6. PubMed PMID: 16941472.
2006
100
Freely downloadable
BEAP
http://www.animalgenome.org/tools/beap/index.html
Provides SNP discovery and analysis of linkage disequilibrium.
Koltes JE, Hu ZL, Fritz E, Reecy JM. BEAP: The BLAST Extension and Alignment Program- a tool for contig construction and analysis of preliminary genome sequence. BMC Res Notes. 2009 Jan 22;2:11. PubMed PMID: 19159488.
2009
100
Freely downloadable
Bovine SNP Retriever
http://www.itb.cnr.it/bovine_snp_retriever/
Retrieves bovine SNPs and related information
Panzitta F, Caprera A, Merelli I, Milanesi L, Williams JL, Lazzari B, Stella A. Mining the bovine genome with the "Bovine SNP Retriever". J Hered. 2008 Nov-Dec;99(6):696-8. Epub 2008 Jun 9. PubMed PMID: 18544553.
2008
100
Online
CandiSNPer
http://www2.hu-berlin.de/wikizbnutztier/software/CandiSNPer/
1) Facilitates the selection of candidate SNPs associated with a disease or another trait of interest. It characterizes SNPs that are located in the vicinity of a start SNP. 2) It computes max LD around start SNP. 3) Information about molecular consequences of SNPs & the genes located in the LD region.
Schmitt AO, Assmus J, Bortfeldt RH, Brockmann GA. CandiSNPer: a web tool for the identification of candidate SNPs for causal variants. Bioinformatics. 2010 Apr 1;26(7):969-70. Epub 2010 Feb 19. PubMed PMID: 20172942.
2010
100
Input- rs ID species-human but regional population specific only. Free, online & user friendly. Divides all SNPs & start SNP into various functional classes like coding, non coding, UTR's, 3' & 5' regions,etc.
Catmap
http://cran.r-project.org/web/packages/catmap/index.html
Nicodemus KK. Catmap: case-control and TDT meta-analysis package. BMC Bioinformatics. 2008 Feb 28;9:130. PubMed PMID: 18307795.
2008
100
Freely downloadable
CLOURE
http://imtech.res.in/~anand/cloure.html
A visualization and exploration environment for non-synonymous coding single nucleotide polymorphisms (nsSNPs) data.
Kohli DK, Bachhawat AK. CLOURE: Clustal Output Reformatter, a program for reformatting ClustalX/ClustalW outputs for SNP analysis and molecular systematics. Nucleic Acids Res. 2003 Jul 1;31(13):3501-2. PubMed PMID: 12824353.
2003
100
URL not working (as on 30 Nov 2013)
CLUMP
http://www.smd.qmul.ac.uk/statgen/dcurtis/software.html
Program designed to assess genetic case-control association studies. It performs: (1) analysis on multiple data files. (2) haplotype phasing. (3) analysis on insertion/deletion polymorphism data. (4) visualizing sliding window results integration with available genome annotations in the UCSC browser.
Not available
Not available
100
Freely downloadable
CLUMPHAP
http://www.smd.qmul.ac.uk/statgen/dcurtis/software.html
1) Performs association analysis of haplotypes to study casual variants. 2) Gives information about SNPs present within genes, which code for drug targets. 3) Provides combined information on drug target proteins (including enzyme, receptor, and agonists/antagonists), genes and SNPs.
Knight J, Curtis D, Sham PC. CLUMPHAP: a simple tool for performing haplotype-based association analysis. Genet Epidemiol. 2008 Sep;32(6):539-45. PubMed PMID: 18395815.
2008
100
Freely downloadable
CNAReporter
not available
Kotliarov Y, Bozdag S, Cheng H, Wuchty S, Zenklusen JC, Fine HA. CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. BMC Med Genomics. 2010 Apr 9;3:11. PubMed PMID: 20380730.
2010
100
-
Crossbow
http://bowtie-bio.sourceforge.net/crossbow/index.shtml
Langmead B, Schatz MC, Lin J, Pop M, Salzberg SL. Searching for SNPs with cloud computing. Genome Biol. 2009;10(11):R134. Epub 2009 Nov 20. PubMed PMID: 19930550.
2009
100
Online
DataBiNS-Viz
A visualization and exploration environment for non-synonymous coding single nucleotide polymorphisms (nsSNPs) data.
Fong CC, Edward AK, Mark DW, Scott JT (2008). DataBiNS-Viz: A Web-Based Tool for Visualization of Non-Synonymous SNP Data. J Proteomics Bioinform 1: 233-236. doi:10.4172/jpb.1000029
Not available
100
-
Drug-SNP
http://ns.nihcgc.re.kr/ ljy75/Drug-SNP.html
1) Provides information about SNPs present within genes, which code for drug targets. 2) Provides combined information on drug target proteins (including enzyme, receptor, and agonists/antagonists), genes and SNPs.
Not available
Not available
100
URL not working (as on 30 Nov 2013)
easyLINKAGE-Plus
http://www.uni-wuerzburg.de/nephrologie/molecular_genetics/molecular_genetics.htm
Hoffmann K, Lindner TH. easyLINKAGE-Plus--automated linkage analyses using large-scale SNP data. Bioinformatics. 2005 Sep 1;21(17):3565-7. Epub 2005 Jul 12. PubMed PMID: 16014370.
2005
100
URL not working (as on 30 Nov 2013)
EICO - Expression-based Imprint Candidate Organizer
http://fantom2.gsc.riken.jp/EICODB/
Nikaido I, Saito C, Wakamoto A, Tomaru Y, Arakawa T, Hayashizaki Y, Okazaki Y. EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D548-51. PubMed PMID: 14681478.
2004
100
URL not working (as on 30 Nov 2013)
FastEpistasis
http://www.vital-it.ch/software/FastEpistasis/
It computes tests of epistasis for a large number of SNP pairs.
Schupbach T, Xenarios I, Bergmann S, Kapur K. FastEpistasis: a high performance computing solution for quantitative trait epistasis. Bioinformatics. 2010 Jun 1;26(11):1468-9. Epub 2010 Apr 7. PubMed PMID: 20375113.
2010
100
Freely downloadable
FastMap
http://cebc.unc.edu/fastmap.html
Performs either single marker mapping (SMM) or haplotype association mapping (HAM) to locate genomic loci associated with a phenotypic variation.
Gatti DM, Shabalin AA, Lam TC, Wright FA, Rusyn I, Nobel AB. FastMap: fast eQTL mapping in homozygous populations. Bioinformatics. 2009 Feb 15;25(4):482-9. Epub 2008 Dec 17. PubMed PMID: 19091771.
2009
100
Freely downloadable. [URL not working (as on 30 Nov 2013)]
Flapjack
http://bioinf.scri.ac.uk/flapjack/
1) For graphical genotyping and haplotype visualization. 2) Based on the input of map, genotype and trait data, it is able to provide a number of alternative graphical genotype views with individual alleles coloured by state, frequency or similarity to a given standard line. 3) Flapjack supports a range of interactions with the data, including graphically moving lines or markers around the display, insertions or deletions of data, and sorting or clustering of lines by either genotype similarity to other lines, or by trait scores. 4) Any map based information such as QTL positions can be aligned against graphical genotypes to identify associated haplotypes.
Milne I, Shaw P, Stephen G, Bayer M, Cardle L, Thomas WT, Flavell AJ, Marshall D. Flapjack--graphical genotype visualization. Bioinformatics. 2010 Dec 15;26(24):3133-4. Epub 2010 Oct 18. PubMed PMID: 20956241.
2010
100
Freely downloadable
F-nsSNP-Syn-Gen
http://sites.google.com/site/compgensite/f-nssnp-syn-gen
Information on experimentally validated functional nsSNPs in human synaptic genes.
Not available
Not available
100
Frequency Finder
http://bluegenes.bsd.uchicago.edu/frequencyfinder/
1) It provides a single, user-friendly interface for retrieving allele frequencies for large batches of SNPs from multiple data sources. 2) To retrieve mapping data and real-time data from the ABI database. 3) Resources for allele frequency data include 3 publicly available databases i.e TSC, dbSNP, ALFRED, HGVbase & Celera genomics. 4) Includes several methods to output the data, including on-screen and as a compressed text file.
Nguyen TH, Liu C, Gershon ES, McMahon FJ. Frequency Finder: a multi-source web application for collection of public allele frequencies of SNP markers. Bioinformatics. 2004 Feb 12;20(3):439-43. Epub 2004 Jan 22. PubMed PMID: 14960477.
2004
100
Online & new version (v2.1) Freely downloadable. [URL not working (as on 30 Nov 2013)]
GCTA
http://gump.qimr.edu.au/gcta/
Analysis of the proportion of phenotypic variance based on the genome/chromosome-wide SNPs for complex traits. 1) Finds the genetic relationship from genome-wide SNPs. 2) Calculates the variance explained by all the autosomal SNPs. 3) Finds the genetic variance associated with the X-chromosome. 4) Estimates the LD structure encompassing a list of target SNPs.
Yang J, Lee SH, Goddard ME, Visscher PM. GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet. 2011 Jan 7;88(1):76-82. Epub 2010 Dec 17. PubMed PMID: 21167468.
2011
100
Freely downloadable
Gene Resource Locator
http://grl.gi.k.u-tokyo.ac.jp
Assembles gene maps, which provide information on gene-expression patterns, cis-elements, alternatively spliced transcript groups, SNP loci, etc.
Honkura T, Ogasawara J, Yamada T, Morishita S. The Gene Resource Locator: gene locus maps for transcriptome analysis. Nucleic Acids Res. 2002 Jan 1;30(1):221-5. PubMed PMID: 11752299.
2002
100
URL not working (as on 30 Nov 2013)
GENECOUNTING
1. http://www.hgmp.mrc.ac.uk/~jzhao 2. http://www.iop.kcl.ac.uk/IoP/Departments/PsychMed/GEpiBSt/software.shtml
Zhao JH. 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics. 2004 May 22;20(8):1325-6. Epub 2004 Feb 10. PubMed PMID: 14871868.
2004
100
1st URL is not working (as on 30 Nov 2013)
genetic map position of SNPs
http://integrin.ucd.ie/cgi-bin/rs2cm.cgi
It is an application, which determines the genetic map position in centiMorgans of SNPs from the Human Genome subset of the dbSNP database.
Not available
Not available
100
Online
Genewindow
http://genewindow.nci.nih.gov/Welcome
Staats B, Qi L, Beerman M, Sicotte H, Burdett LA, Packer B, Chanock SJ, Yeager M. Genewindow: an interactive tool for visualization of genomic variation. Nat Genet. 2005 Feb;37(2):109-10. PubMed PMID: 15678133.
2005
100
Online
GENOME
http://www.sph.umich.edu/csg/liang/genome/
Liang L, Zollner S, Abecasis GR. GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics. 2007 Jun 15;23(12):1565-7. Epub 2007 Apr 25. PubMed PMID: 17459963.
2007
100
Freely downloadable. [URL not working (as on 30 Nov 2013)]
GENOTRACE
http://genotrace.niob.knaw.nl/
Used in genetic studies to analyze individuals for codon-changing single nucleotide polymorphisms or mutations.
Berezikov E, Plasterk RH, Cuppen E. GENOTRACE: cDNA-based local GENOme assembly from TRACE archives. Bioinformatics. 2002 Oct;18(10):1396-7. PubMed PMID: 12376385.
2002
100
Online
GenotypeColour
http://www.med.unibs.it/~barlati/GenotypeColour/
Provides coloured visualization, which is useful in displaying and comparing SNP and CNV genomic data.
Barlati S, Chiesa S, Magri C. "GenotypeColour": colour visualisation of SNPs and CNVs. BMC Bioinformatics. 2009 Feb 4;10:49. PubMed PMID: 19193232.
2009
100
Freely downloadable
GenoWatch
http://genepipe.ngc.sinica.edu.tw/genowatch
A bioinformatics pipeline for large-scale human genomic variation studies.
Chen YH, Liu CK, Chang SC, Lin YJ, Tsai MF, Chen YT, Yao A. GenoWatch: a disease gene mining browser for association study. Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W336-40. Epub 2008 Apr 25. PubMed PMID: 18440974
2008
100
Online
GEN-SNiP
www.argusbio.com/sooryakiran/gensnip/gensnip.php
Identifies variations in a set of test DNA sequences with respect to a standard reference sequence and generates a list of substitutions, insertions and deletions for each test sequences.
Whyte DB, Nair GG, Nair AS, Oommen OV. GEN-SNiP: an online tool to find polymorphisms in a genome. In Silico Biol. 2009;9(5-6):333-6. doi: 10.3233/ISB-2009-0401. PubMed PMID: 22430435
Not available
100
URL not working (as on 30 Nov 2013)
GEVALT - GEnotype Visualization and ALgorithmic Tool
http://acgt.cs.tau.ac.il/gevalt/
Performs genotype phasing, tag SNP selection, LD and haplotype block- analysis, association tests and visual display.
Davidovich O, Kimmel G, Shamir R. GEVALT: an integrated software tool for genotype analysis. BMC Bioinformatics. 2007 Feb 1;8:36. PubMed PMID: 17270038.
2007
100
Freely downloadable. Requires installation of JRE v1.5 or later version.
Retrieves genome-wide inter-SNP associations and explores LD patterns for any number of SNPs of interest and can be useful in identifying SNPs with long-range LD.
Lawrence R, Day-Williams AG, Mott R, Broxholme J, Cardon LR, Zeggini E. GLIDERS--a web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs. BMC Bioinformatics. 2009 Oct 31;10:367. PubMed PMID: 19878600.
2009
100
Online. [URL not working (as on 30 Nov 2013)]
GOLDsurfer
www.umbio.com
A java-based analysis and graphics program for three-dimensional plotting of linkage disequilibrium (LD) and facilitates the interpretation of LD patterns. It is embedded with the Evince graphical software package.
Pettersson F, Jonsson O, Cardon LR. GOLDsurfer: three dimensional display of linkage disequilibrium. Bioinformatics. 2004 Nov 22;20(17):3241-3. Epub 2004 Jun 16. PubMed PMID: 15201180.
2004
100
Online registration
GSA-SNP
http://gsa.muldas.org/
1)The gene set analysis methods were introduced to GWA studies to address the association of gene sets that share common biological functions. 2) A general approach for GSA in GWA analysis and a stand-alone software GSA-SNP that implements three widely used GSA methods.
Nam D, Kim J, Kim SY, Kim S. GSA-SNP: a general approach for gene set analysis of polymorphisms. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W749-54. Epub 2010 May 25. PubMed PMID: 20501604.
2010
100
Freely downloadable
GSEA-SNP
http://www.nr.no/pages/samba/area_emr_smbi_gseasnp
Analysis of the SNP data from association studies by the application of gene set enrichment analysis (GSEA) method.
Holden M, Deng S, Wojnowski L, Kulle B. GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies. Bioinformatics. 2008 Dec 1;24(23):2784-5. Epub 2008 Oct 14. PubMed PMID: 18854360.
2008
100
Freely downloadable
GWAS GUI
http://www.sph.umich.edu/csg/weich/browser/
Chen W, Liang L, Abecasis GR. GWAS GUI: graphical browser for the results of whole-genome association studies with high-dimensional phenotypes. Bioinformatics. 2009 Jan 15;25(2):284-5. Epub 2008 Nov 20. PubMed PMID: 19028721.
2009
100
Freely downloadable
GWAsimulator
http://biostat.mc.vanderbilt.edu/wiki/Main/GWAsimulator
It can simulate the genotype data for SNP chips that are used in genome-wide association (GWA) studies and provides more detailed LD information for case-control data or population samples.
Li C, Li M. GWAsimulator: a rapid whole-genome simulation program. Bioinformatics. 2008 Jan 1;24(1):140-2. Epub 2007 Nov 15. PubMed PMID: 18006546.
2008
100
Freely downloadable
HapBlock
http://www.cmb.usc.edu/msms/HapBlock/
1) Estimates the block partition with minimum number of tag SNPs for the given criteria of blocks and tag SNPs. 2) Both haplotype data and genotype data from unrelated individuals and/or from general pedigrees can be analyzed. 3) The programs provide flexibility to include specific SNPs (e.g. non-synonymous SNPs) as tag SNPs. 4) It incorporates different definitions of haplotype block and different criteria for tag SNP selections for different applications. 5) It provides an interface that can take the output from other methods for haplotype block partitioning and tag SNP selection as input.
Zhang K, Qin Z, Chen T, Liu JS, Waterman MS, Sun F. HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms. Bioinformatics. 2005 Jan 1;21(1):131-4. Epub 2004 Aug 27. PubMed PMID: 15333454.
2005
100
Freely downloadable
hapConstructor
http://bioinformatics.med.utah.edu/Genie/hapConstructor.html
Abo R, Knight S, Wong J, Cox A, Camp NJ. hapConstructor: automatic construction and testing of haplotypes in a Monte Carlo framework. Bioinformatics. 2008 Sep 15;24(18):2105-7. Epub 2008 Jul 23. PubMed PMID: 18653522.
2008
100
Freely downloadable. [URL not working (as on 30 Nov 2013)]
HaploBuild
http://snp.bumc.bu.edu/modules.php?name=HaploBuild
Builds haplotype by allowing the association of subsets of single nucleotide polymorphisms (SNPs).
Laramie JM, Wilk JB, DeStefano AL, Myers RH. HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies. Bioinformatics. 2007 Aug 15;23(16):2190-2. Epub 2007 Jun 22. PubMed PMID: 17586827.
2007
100
Freely downloadable. [URL not working (as on 30 Nov 2013)]
HaploSNPer
http://www.bioinformatics.nl/tools/haplosnper/
Detects SNPs and alleles in the user-specified input sequences from both diploid and polyploid species.
Tang J, Leunissen JA, Voorrips RE, van der Linden CG, Vosman B. HaploSNPer: a web-based allele and SNP detection tool. BMC Genet. 2008 Feb 28;9:23. PubMed PMID: 18307806.
2008
100
Online
HAPLOT
http://krunch.med.yale.edu/haplo/
Compares variations in linkage disequilibrium patterns, in tagSNP sets, and in SNP heterozygosities among populations, which can be useful to infer the evolutionary patterns among different populations.
Gu S, Pakstis AJ, Kidd KK. HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations. Bioinformatics. 2005 Oct 15;21(20):3938-9. Epub 2005 Aug 30. PubMed PMID: 16131520.
2005
100
Freely downloadable
HapScope
http://lpg.nci.nih.gov/lpg_small/protocols/HapScope/
Zhang J, Rowe WL, Struewing JP, Buetow KH. HapScope: a software system for automated and visual analysis of functionally annotated haplotypes. Nucleic Acids Res. 2002 Dec 1;30(23):5213-21. PubMed PMID: 12466546.
2002
100
The website is temporarily unavailable due to maintenance work (as on 4 Dec 2013)
HEPTAPLEX SNP
NOT AVAILABLE
Provides allele frequency data of the South-West Poland population.
Not available
Not available
100
-
InSNP
http://www.mucosa.de/insnp/
Detects and provides compact visualization of the substitution and indel SNPs in sequencing traces.
Manaster C, Zheng W, Teuber M, Wächter S, Döring F, Schreiber S, Hampe J. InSNP: a tool for automated detection and visualization of SNPs and InDels. Hum Mutat. 2005 Jul;26(1):11-9. PubMed PMID: 15931688.
2005
100
Online registration
INTERSNP
http://intersnp.meb.uni-bonn.de/
Provides a genome-wide interaction analysis of the case-control SNP data.
Herold C, Steffens M, Brockschmidt FF, Baur MP, Becker T. INTERSNP: genome-wide interaction analysis guided by a priori information. Bioinformatics. 2009 Dec 15;25(24):3275-81. Epub 2009 Oct 16. PubMed PMID: 19837719.
2009
100
Freely downloadable
is-rSNP
http://enzyme.msd.nicta.com.au/is-rSNP/index.html
Detects SNP in the regulatory region i.e. whether it is affecting the transcription factor binding site or not.
Macintyre G, Bailey J, Haviv I, Kowalczyk A. is-rSNP: a novel technique for in silico regulatory SNP detection. Bioinformatics. 2010 Sep 15;26(18):i524-30. PubMed PMID: 20823317.
2010
100
Online registration
KinSNP
http://bioinfo.bgu.ac.il/bsu/software/KinSNP/
1) For homozygosity mapping in families having the same lineage using SNP arrays. 2) It combines microarray genotype calls with the most updated SNP annotations, and searches for stretches of SNPs which are homozygous to the same allele in all ascertained sick individuals. (The input is- SNPs with rs ids & chromosome position & snp chip data).
Amir el-AD, Bartal O, Morad E, Nagar T, Sheynin J, Parvari R, Chalifa-Caspi V. KinSNP software for homozygosity mapping of disease genes using SNP microarrays. Hum Genomics. 2010 Aug;4(6):394-401. PubMed PMID: 20846928.
2010
100
Freely downloadable
LD2SNPing
http://bio.kuas.edu.tw/LD2NPing
Provides SNP ID- and gene-centric online retrievals for SNP information, tag SNPs, provides RFLP enzyme information for SNP genotype and performs LD analysis.
Chang HW, Chuang LY, Chang YJ, Cheng YH, Hung YC, Chen HC, Yang CH. LD2SNPing: linkage disequilibrium plotter and RFLP enzyme mining for tag SNPs. BMC Genet. 2009 Jun 6;10:26. PMID:19500380
2009
100
URL not working (as on 30 Nov 2013)
LDA - Linkage disequilibrium analyzer
http://www.chgb.org.cn/lda/lda.htm
Ding K, Zhou K, He F, Shen Y. LDA--a java-based linkage disequilibrium analyzer. Bioinformatics. 2003 Nov 1;19(16):2147-8. PMID:14594722
2003
100
URL not working (as on 30 Nov 2013)
LDB2000
http://cedar.genetics.soton.ac.uk/public html/LDB2000.html
Information on sequence based integrated maps, which provide locations for genes and polymorphic markers in sequence and on genetic linkage, radiation hybrid and cytogenetic scales.
Ke X, Tapper W, Collins A. LDB2000: sequence-based integrated maps of the human genome. Bioinformatics. 2001 Jul;17(7):581-6. PMID:11448876
2001
100
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LdCompare
http://www.affymetrix.com/support/developer/tools/devnettools.affx
A program that characterizes whole-genome LD structure on large number of SNPs in terms of single- and multiple-marker correlations.
Hao K, Di X, Cawley S. LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage. Bioinformatics. 2007 Jan 15;23(2):252-4. Epub 2006 Dec 5. PMID:17148510
2007
100
Online registration
LD-Plus
https://chgr.mc.vanderbilt.edu/ldplus/create/setparams
1) It is a visualization tool for display of single SNP statistics in the context of linkage disequilibrium and haplotype structures. 2) It also displays continuous and categorical SNP statistics. 3) It parses Haploview output to display both D' and r blocks, and haplotype frequencies. LD-Plus can display both continuous and categorical SNP statistics, and r2 LD plots.
Bush WS, Dudek SM, Ritchie MD. Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus. Bioinformatics. 2010 Feb 15;26(4):578-9. Epub 2010 Feb 3. PMID:20130027
2010
100
Online
Libsequence
http://www.molpopgen.org/software/libsequence.html
A C++ library, which is designed to aid in writing applications for genomics and evolutionary genetics and performs the analysis of SNP data and sequence divergence.
Thornton K. Libsequence: a C++ class library for evolutionary genetic analysis. Bioinformatics. 2003 Nov 22;19(17):2325-7. PMID:14630667
2003
100
Freely downloadable
LS-SNP/PDB
http://ls-snp.icm.jhu.edu/ls-snp-pdb/
Provides information useful for identifying amino-acid changing SNPs (nsSNPs) that have an impact on biological function.
Ryan M, Diekhans M, Lien S, Liu Y, Karchin R. LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. Bioinformatics. 2009 Jun 1;25(11):1431-2. Epub 2009 Apr 15. PMID:19369493
2009
100
Online
MapNext
http://evolution.sysu.edu.cn/english/software/mapnext.htm
A comprehensive tool for both spliced and unspliced alignments of short reads and automated SNP detection from population sequences.
Bao H, Xiong Y, Guo H, Zhou R, Lu X, Yang Z, Zhong Y, Shi S. MapNext: a software tool for spliced and unspliced alignments and SNP detection of short sequence reads. BMC Genomics. 2009 Dec 3;10 Suppl 3:S13. PMID:19958476
2009
100
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MAP-O-MAT
http://compgen.rutgers.edu/mapomat/
Provides automated linkage mapping of human polymorphic DNA markers.
Kong X, Matise TC. MAP-O-MAT: internet-based linkage mapping. Bioinformatics. 2005 Feb 15;21(4):557-9. Epub 2004 Sep 16. PMID:15374870
2005
100
Online
MAVIANT
http://snp.agrsci.dk/maviant
Panitz F, Stengaard H, Hornshøj H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, Høj A, Vingborg RK, Zahn B, Wang X, Wang X, Wernersson R, Jorgensen CB, Scheibye-Knudsen K, Arvin T, Lumholdt S, Sawera M, Green T, Nielsen BJ, Havgaard JH, Brunak S, Fredholm M, Bendixen C. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation. Bioinformatics. 2007 Jul 1;23(13):i387-91. PubMed PMID: 17646321.
2007
100
URL not working (as on 30 Nov 2013)
MedRefSNP
http://www.medclue.com/ medrefsnp
Provides enhanced and integrated information of the published SNPs by using its genomic and functional aspects.
Rhee H, Lee JS. MedRefSNP: a database of medically investigated SNPs. Hum Mutat. 2009 Mar;30(3):E460-6. PMID:19105187
2009
100
URL not working (as on 30 Nov 2013)
MicroSNiPer
http://cbdb.nimh.nih.gov/microsniper/
It examines the 3'-untranslated region and predicts if a SNP within the target site will disrupt or enhance a microRNA binding site.
Barenboim M, Zoltick BJ, Guo Y, Weinberger DR. MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. Hum Mutat. 2010 Nov;31(11):1223-32. doi: 10.1002/humu.21349. Epub 2010 Oct 7. PMID: 20809528
2010
100
Online
Minimotif miner 2nd release
http://mnm.engr.uconn.edu
Assists in the prediction of motif-based functions in user-supplied protein queries and also provides expanded SNP analysis.
Rajasekaran S, Balla S, Gradie P, Gryk MR, Kadaveru K, Kundeti V, Maciejewski MW, Mi T, Rubino N, Vyas J, Schiller MR. Minimotif miner 2nd release: a database and web system for motif search. Nucleic Acids Res. 2009 Jan;37(Database issue):D185-90. Epub 2008 Oct 31. PubMed PMID: 18978024.
2009
100
Online
MOCSphaser
http://emu.src.riken.jp/
1) Finds frequencies of haplotypes composed of allelic copy numbers and SNP alleles at multiple CNV and SNP loci from the Mixture-data-Of-Cnv-Snp. 2) Also, calculates individual diplotypes and its respective frequencies. 3) Finds diplotype frequencies calculated from the haplotype frequencies under Hardy-Weinberg equilibrium.
Kato M, Nakamura Y, Tsunoda T. MOCSphaser: a haplotype inference tool from a mixture of copy number variation and single nucleotide polymorphism data. Bioinformatics. 2008 Jul 15;24(14):1645-6. Epub 2008 May 20. PubMed PMID: 18492685.
2008
100
Freely downloadable
Mouse SNP Miner
http://bioinfo.embl.it/SnpApplet/
Detailed information on the mouse functional SNPs and comprises of a runtime graphical display that allows chromosome walking, in-and-out zooming, and jumping between adjacent SNPs.
Reuveni E, Ramensky VE, Gross C. Mouse SNP Miner: an annotated database of mouse functional single nucleotide polymorphisms. BMC Genomics. 2007 Jan 21;8:24. PubMed PMID: 17239255.
2007
100
Online (needs JAVA platform)
MQScore_SNP
http://mga.bionet.nsc.ru/soft/MQscore_SNP/
Performs multipoint parametric linkage analysis of quantitative traits using SNPs in large pedigrees without loops (linkage of triats, which are affected by multiple genes is studied by SNP markers/genotypes of large pedigree).
Axenovich TI, Aulchenko YS. MQScore_SNP software for multipoint parametric linkage analysis of quantitative traits in large pedigrees. Ann Hum Genet. 2010 May;74(3):286-9. PubMed PMID: 20529018.
2010
100
Freely downloadable
MutaGeneSys
http://www1.cs.columbia.edu/~jds1/MutaGeneSys/
It uses genome-wide genotype data to estimate individual disease susceptibility; it accepts SNP data of individuals as query input and delivers disease susceptibility hypotheses.
Stoyanovich J, Pe'er I. MutaGeneSys: estimating individual disease susceptibility based on genome-wide SNP array data. Bioinformatics. 2008 Feb 1;24(3):440-2. Epub 2007 Nov 29. PubMed PMID: 18048395.
2008
100
Freely downloadable
Mutation Checker
http://mutation.sanbi.ac.za/checker
Not available
Not available
100
URL not working (as on 30 Nov 2013)
Mutation@A Glance
http://rapid.rcai.riken.jp/mutation/
A tool for mutation analysis of causative genes of human diseases.
Hijikata A, Raju R, Keerthikumar S, Ramabadran S, Balakrishnan L, Ramadoss SK, Pandey A, Mohan S, Ohara O. Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. DNA Res. 2010 Jun;17(3):197-208. Epub 2010 Apr 1. PubMed PMID: 20360267.
2010
100
Online
URL not working (as on 24 April 2014)
novoSNP
http://www.molgen.ua.ac.be/bioinfo/novosnp/
Detects variations (SNPs and short INDELs) in resequencing projects. It takes a reference sequence and a number of sequencing trace files as input, and generates a list of possible variations with a quality score and also allows the user to easily filter, sort and check the variations (visually).
Weckx S, Del-Favero J, Rademakers R, Claes L, Cruts M, De Jonghe P, Van Broeckhoven C, De Rijk P. novoSNP, a novel computational tool for sequence variation discovery. Genome Res. 2005 Mar;15(3):436-42. PubMed PMID: 15741513.
2005
100
Freely downloadable
Panseq
http://76.70.11.198/panseq
Finds SNPs within the core genome of the pan-genome and also determines the distribution of accessory genomic regions.
Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A, Villegas A, Thomas JE, Gannon VP. Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics. 2010 Sep 15;11:461. PubMed PMID: 20843356.
2010
100
Online
ParaHaplo
http://en.sourceforge.jp/projects/parallelgwas/releases/
Conducts haplotype-based genome-wide association studies and analyzes the multiple comparisons at multiple SNP loci in linkage disequilibrium by treating linked loci as one haplotype block.
Misawa K, Kamatani N. ParaHaplo 2.0: a program package for haplotype-estimation and haplotype-based whole-genome association study using parallel computing. Source Code Biol Med. 2010 Jun 4;5:5. PubMed PMID: 20525312.
2010
100
Freely downloadable
A tool for the display and analysis of polymorphisms in genes. It uses a reference DNA sequence, an exon/intron position model and a list of polymorphisms to determine the effects of these polymorphisms on the expressed gene product, as well as the changes in restriction enzyme recognition sites.
Taylor NE, Greene EA. PARSESNP: A tool for the analysis of nucleotide polymorphisms. Nucleic Acids Res. 2003 Jul 1;31(13):3808-11. PubMed PMID: 12824424.
2003
100
Online
Path
http://genapha.icapture.ubc.ca/PathTutorial/
Provides information on SNPs and genetic association studies, which are collected from different online resources.
Zamar D, Tripp B, Ellis G, Daley D. Path: a tool to facilitate pathway-based genetic association analysis. Bioinformatics. 2009 Sep 15;25(18):2444-6. Epub 2009 Jul 23. PubMed PMID: 19628508.
2009
100
Freely downloadable
pfSNP
http://pfs.nus.edu.sg/%28S%28xnqct0xfimmbnwwr2yw53lec%29%29/PFS_LogIn_V2.aspx
1) Finds putative function of the SNP and also projects whether the SNP has previously been associated with similar or other diseases/phenotypes/functions. 2) To select potentially functional SNPs in any gene-of-interest for studies associating a particular gene with phenotype. 3) Provides information on other previous reports that have examined the SNP-of-interest. 4) Provides information regarding the highest LD values (r2) of nearby pfSNPs.
Wang J, Ronaghi M, Chong SS, Lee CG. pfSNP: An integrated potentially functional SNP resource that facilitates hypotheses generation through knowledge syntheses. Hum Mutat. 2011 Jan;32(1):19-24. doi: 10.1002/humu.21331. PubMed PMID: 20672376.
2011
100
Registration required
PGA - Power for Genetic Association analyses
http://dceg.cancer.gov/bb/tools/pga
A package of algorithms and graphical user interfaces developed in Matlab for power and sample size calculation under various genetic models and statistical constraints.
Menashe I, Rosenberg PS, Chen BE. PGA: power calculator for case-control genetic association analyses. BMC Genet. 2008 May 13;9:36. PubMed PMID: 18477402.
2008
100
The website states that users without Matlab software should install first the MATLAB Component Runtime (MCR) on their computers.
PicSNP
http://picsnp.org
Chang H, Fujita T. PicSNP: a browsable catalog of nonsynonymous single nucleotide polymorphisms in the human genome. Biochem Biophys Res Commun. 2001 Sep 14;287(1):288-91. PubMed PMID: 11549289.
2001
100
Page not working (as on 30 Nov 2013)
PolyDoms
http://polydoms.cchmc.org/polydoms/
Provides a method to derive a list of candidate SNPs, which can be evaluated in experimental or epidemiological studies for the impact on protein functions and disease risk associations.
Jegga AG, Gowrisankar S, Chen J, Aronow BJ. PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease. Nucleic Acids Res. 2007 Jan;35(Database issue):D700-6. Epub 2006 Nov 16. PubMed PMID: 17142238.
2007
100
URL not working (as on 30 Nov 2013)
PolyScan
http://genome.wustl.edu/pub/software/polyscan/
Predicts the affect of an amino acid substitution on protein function. [The input is a-protein sequence & amino acid, which is substituted by another & position of amino acid in the protein sequence].
Chen K, McLellan MD, Ding L, Wendl MC, Kasai Y, Wilson RK, Mardis ER. PolyScan: an automatic indel and SNP detection approach to the analysis of human resequencing data. Genome Res. 2007 May;17(5):659-66. Epub 2007 Apr 6. PubMed PMID: 17416743.
2007
100
Online
POPTREE2
http://www.kms.ac.jp/~genomelb/takezaki/poptree2
Constructs phylogenetic trees from allele frequency data and also measures genetic variation in a population and genetic differentiation among subdivided populations.
Takezaki N, Nei M, Tamura K. POPTREE2: Software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol. 2010 Apr;27(4):747-52. Epub 2009 Dec 18. PubMed PMID: 20022889.
2010
100
Installation required.
Promolign
http://polly.wustl.edu/promolign/main.html
Information on the correlation of SNPs with the TF sites, which assists in the functional evaluation of SNPs and provides graphical presentation for SNPs and transcription factor binding sites in the promoter region of genes in context to human-mouse orthologous sequence alignment.
Zhao T, Chang LW, McLeod HL, Stormo GD. PromoLign: a database for upstream region analysis and SNPs. Hum Mutat. 2004 Jun;23(6):534-9. PubMed PMID: 15146456.
2004
100
URL not working (as on 30 Nov 2013)
PupasView
http://pupasview.ochoa.fib.es http://www.pupasnp.org.
Provides information on the phenotypic effects caused by SNPs at both the translational and the transcriptional level.
Conde L, Vaquerizas JM, Ferrer-Costa C, de la Cruz X, Orozco M, Dopazo J. PupasView: a visual tool for selecting suitable SNPs, with putative pathological effect in genes, for genotyping purposes. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W501-5. PubMed PMID: 15980522
2005
100
QuickSNP
http://bioinformoodics.jhmi.edu/quickSNP.pl
Provides an option to select only gene-centric SNPs from a chromosomal region in an automated fashion. Other useful features include SNP filtering based on inter-SNP distances and information regarding the availability of genotyping assays for SNPs and whether they are present on whole genome chips.
Grover D, Woodfield AS, Verma R, Zandi PP, Levinson DF, Potash JB. QuickSNP: an automated web server for selection of tagSNPs. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W115-20. Epub 2007 May 21. PubMed PMID: 17517769.
2007
100
URL not working (as on 28 Nov 2013)
Seq4SNPs
http://www.srl.cam.ac.uk/oncology/bio/s4shome.html
Incorporates annotation for SNPs and repetitive elements and assists in the SNP-genotyping.
Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design. Field HI, Scollen SA, Luccarini C, Baynes C, Morrison J, Dunning AM, Easton DF, Pharoah PD. BMC Bioinformatics. 2009 Jun 12;10:180.
2009
100
Message displayed that the new URL for the resource will be updated soon (as on 30 Nov 2013)
SeqDoC- Sequence Difference of Chromatograms
http://research.imb.uq.edu.au/seqdoc/
Allows comparison of ABI sequence chromatograms, which helps in the rapid identification of SNPs and point mutations and also highlights different characteristic of single base changes, including heterozygous SNPs and insertions and deletions.
Crowe ML. SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms. BMC Bioinformatics. 2005 May 31;6:133. PubMed PMID: 15927052.
2005
100
Online
Seq-SNPing
http://bio.kuas.edu.tw/Seq-SNPing
A sequence alignment program, which incorporates SNP identification tools for association studies.
Chang HW, Chuang LY, Cheng YH, Ho CH, Wen CH, Yang CH. Seq-SNPing: multiple-alignment tool for SNP discovery, SNP ID identification, and RFLP genotyping. OMICS. 2009 Jun;13(3):253-60. PubMed PMID: 19514837.
2009
100
It requires the Java Running Environment (JRE 1.5.0) to run properly.
SimHap GUI
not available
An integrated graphical analysis tool for conducting epidemiological, single SNP and haplotype-based association analysis.
Carter KW, McCaskie PA, Palmer LJ. SimHap GUI: an intuitive graphical user interface for genetic association analysis. BMC Bioinformatics. 2008 Dec 25;9:557. PubMed PMID: 19109877.
2008
100
Online
SKM-SNP
http://www.math.hkbu.edu.hk/~mng/SKM-SNP/SKM-SNP.html
It is a SNP marker detection program, which identifies a set of relevant SNPs for the association between a disease and multiple marker genotypes.
Liu Y, Li M, Cheung YM, Sham PC, Ng MK. SKM-SNP: SNP markers detection method. J Biomed Inform. 2010 Apr;43(2):233-9. Epub 2009 Nov 17. PubMed PMID: 19925882.
2010
100
-
Snap - Single Nucleotide Polymorphism Annotation Platform
http://snap.genomics.org.cn/
1)Performs detailed analysis of human genes and their variations. The input can be-gene name, chromosome location, marker position, clone & SNP rs ids. 2)Provides a gene-gene relationship network on protein-protein interaction data, metabolic pathway connections and phylogenetic relations. 3) Assits in primer designing for amplification/seqeuncing of cDNA, genomic DNA, introns or exons. 4) Information on SNPs affecting RNA splicing, types of SNPs (synonymus, non-synonymus & in-dels), regions where SNP is present in the gene/genome region.
Li S, Ma L, Li H, Vang S, Hu Y, Bolund L, Wang J. Snap: an integrated SNP annotation platform. Nucleic Acids Res. 2007 Jan;35(Database issue):D707-10. Epub 2006 Nov 29. PubMed PMID: 17135198.
2007
100
Program files available for download.
SNAP - Screening for non-acceptable polymorphisms
http://www.rostlab.org/services/SNAP
Evaluates the effects of single amino acid substitutions on protein function.
Bromberg Y, Rost B. SNAP: predict effect of non-synonymous polymorphisms on function. Nucleic Acids Res. 2007;35(11):3823-35. Epub 2007 May 25. PubMed PMID: 17526529.
2007
100
Online. It returns its results to the user via e-mail.
SNEP - Simultaneous detection of both nucleotide and expression polymorphisms
http://www.ism.ac.jp/~fujisawa/SNEP/
It is a R-software, which facilitates the detection of both nucleotide and expression polymorphisms simultaneously.
Fujisawa H, Horiuchi Y, Harushima Y, Takada T, Eguchi S, Mochizuki T, Sakaguchi T, Shiroishi T, Kurata N. SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip. BMC Bioinformatics. 2009 May 6;10:131. PubMed PMID: 19419536.
2009
100
Online
SNP Chart
http://www.snpchart.ca
Tebbutt SJ, Opushnyev IV, Tripp BW, Kassamali AM, Alexander WL, Andersen MI. SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data. Bioinformatics. 2005 Jan 1;21(1):124-7. Epub 2004 Aug 12. PubMed PMID: 15308543.
2005
100
Page not responding as on (28 Nov 2013).
SNP cherry picker
Author ID: SD@oxagen.co.uk
Assists in finding SNPs associated with an increased risk of disease.
Harris M, Martin JM, Peden JF, Rawlings CJ. SNP cherry picker: maximizing the chance of finding an association with a disease SNP. Bioinformatics. 2003 Nov 1;19(16):2141-3. PubMed PMID: 14594720.
2003
100
The reporting article claims that the software is available, free of charge, for academic use on request from the authors.
SNP Cutter
http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm
Designs primers for either natural PCR-RFLP or mismatch PCR-RFLP, to perform the assay on a batch of SNPs from the human genome.
Zhang R, Zhu Z, Zhu H, Nguyen T, Yao F, Xia K, Liang D, Liu C. SNP Cutter: a comprehensive tool for SNP PCR-RFLP assay design. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W489-92. PubMed PMID: 15980518.
2005
100
URL not working (as on 28 Nov 2013)
SNP ID-info
http://bio.kuas.edu.tw/snpid-info
Provides an SNP ID by inputting the primers, genomic sequence, chromosome contig range and cytogenic band information for human, rat and mouse sequences with or without primers and serves to be a helpful platform for systematic SNP association studies.
Yang CH, Chuang LY, Cheng YH, Wen CH, Chang PL, Chang HW. SNP ID-info: SNP ID searching and visualization platform. OMICS. 2008 Sep;12(3):217-26. PubMed PMID: 18582176.
2008
100
Online
snp.plotter
http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html
1) Produces images of genetic association results using single SNP and/or haplotype data with a corresponding LD heatmap in one correctly aligned graphic. 2) Plots single SNP and/or haplotype data and simultaneously plot multiple sets of results. 3) Figures are produced in two print sizes (3.5 and 7 inches) corresponding to one and two columns, respectively, on a printed page in resolution-independent formats (PDF and EPS) for ease of use in manuscript preparation. 4) Its figures can be easily imported into LaTeX documents, and due to the resolution-independent formats used, figures can be converted into raster image formats such as JPG, PNG and BMP without a loss in quality. 5) It includes options to display a linkage disequilibrium (LD) plot below the P-value plot using either the r2 or D0 LD metric, to set the X-axis to equal spacing or to use the physical map of markers, and to specify plot labels, colors, symbols and LD heatmap color scheme.
Luna A, Nicodemus KK. snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package. Bioinformatics. 2007 Mar 15;23(6):774-6. Epub 2007 Jan 18. PubMed PMID: 17234637.
2007
100
Freely downloadable
SNP@Domain
http://snpnavigator.net/
Finds SNPs within protein domains with 2D and 3D maps and this visual annotation of SNPs is useful to interpret SNPs associated with diseases.
Han A, Kang HJ, Cho Y, Lee S, Kim YJ, Gong S. SNP@Domain: a web resource of single nucleotide polymorphisms (SNPs) within protein domain structures and sequences. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W642-4. PubMed PMID: 16845090.
2006
100
Page not responding (as on 28 Nov 2013)
SNP@Ethnos
http://variome.kobic.re.kr/SNPatETHNIC/
Finds the ethnically variant single-nucleotide polymorphisms (ESNPs) from the genotype profile of the populations included in the International HapMap database.
Park J, Hwang S, Lee YS, Kim SC, Lee D. SNP@Ethnos: a database of ethnically variant single-nucleotide polymorphisms. Nucleic Acids Res. 2007 Jan;35(Database issue):D711-5. Epub 2006 Nov 28. PubMed PMID: 17135185.
2007
100
Online
SNP@Evolution
http://bighapmap.big.ac.cn/
Integrates the heterozygosity (HET) of SNPs based on data of HapMap with the available data of integrated Haplotype Score (iHS) at levels of single SNPs, genes, and regions of chromosomes and focuses on the positive selection of the human genome.
Cheng F, Chen W, Richards E, Deng L, Zeng C. SNP@Evolution: a hierarchical database of positive selection on the human genome. BMC Evol Biol. 2009 Sep 5;9:221. PubMed PMID: 19732458
2009
100
Online & data can be downloaded for hapmap phase project.
SNP@Promoter
http://variome.kobic.re.kr/SNPatPromoter
Identifies functional SNPs in the putative promoter regions. The database can be searched by three entries like- a) SNP identifier (rs number from dbSNP), b) by gene (gene name, gene symbol, refSeq ID), and c) by disease term.
Kim BC, Kim WY, Park D, Chung WH, Shin KS, Bhak J. SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions. BMC Bioinformatics. 2008;9 Suppl 1:S2. PubMed PMID: 18315851.
2008
100
URL not working (as on 28 Nov 2013)
SNP_tools
http://www.bioinformatics.org/snp-tools-excel/
Provides a basic genetic and epidemiological analysis of the SNP data and serves as a general add-in for the Microsoft Excel.
Chen B, Wilkening S, Drechsel M, Hemminki K. SNP_tools: A compact tool package for analysis and conversion of genotype data for MS-Excel. BMC Res Notes. 2009 Oct 23;2:214. PubMed PMID: 19852806.
2009
100
-
SNP2CAPS
http://pgrc.ipk-gatersleben.de/snp2caps/
Provides detection of SNPs and Indels and facilitates the computational conversion of SNPs to CAPS (cleaved amplified polymorphic sequences) markers.
Thiel T, Kota R, Grosse I, Stein N, Graner A. SNP2CAPS: a SNP and INDEL analysis tool for CAPS marker development. Nucleic Acids Res. 2004 Jan 2;32(1):e5. PubMed PMID: 14704362.
2004
100
-
SNP2RFLP
http://genetics.bwh.harvard.edu/snp2rflp/
Extracts region-specific SNPs from the NCBI mouse SNP database, which are informative between the mouse strains and further identifies those SNPs that create restriction fragment length polymorphisms (RFLPs).
Beckstead WA, Bjork BC, Stottmann RW, Sunyaev S, Beier DR. SNP2RFLP: a computational tool to facilitate genetic mapping using benchtop analysis of SNPs. Mamm Genome. 2008 Oct-Dec;19(10-12):687-90. Epub 2008 Oct 29. PubMed PMID: 18958524.
2008
100
Freely downloadable
SNPAnalyzer
http://snp.istech.info/istech/board/login_form.jsp
Yoo J, Seo B, Kim Y. SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W483-8. PubMed PMID: 15980517
2005
100
Online registration
SNPannotator
http://dna.leeds.ac.uk/snpannotator/
Provides physical as well as genetic map positions to SNPs, which are present in the Affymetrix genotype data.
Not available
Not available
100
Freely downloadable
SNPator
http://www.snpator.org/public/new_login/index.php
Performs the analysis of SNPs along with associated genomic information (e. g. chromosome position).
Morcillo-Suarez C, Alegre J, Sangros R, Gazave E, de Cid R, Milne R, Amigo J, Ferrer-Admetlla A, Moreno-Estrada A, Gardner M, Casals F, Perez-Lezaun A, Comas D, Bosch E, Calafell F, Bertranpetit J, Navarro A. SNP analysis to results (SNPator): a web-based environment oriented to statistical genomics analyses upon SNP data. Bioinformatics. 2008 Jul 15;24(14):1643-4. Epub 2008 May 30. PubMed PMID: 18515823.
2008
100
Online registration
SNPbox
http://www.snpbox.org/cgi-box/SNPbox.cgi
1) Primers are designed for a well-defined target sequence, which can contain either known SNPs from public databases for validation (SNP module), coding regions indicated by aligning cDNA/EST sequences to the genomic DNA (exon module), or promoter or whole genomic regions (saturation module). 2) It has an interface to a local database where primer information of the genome-wide application can be retrieved. 3) The genomic sequence is aligned to a local copy of HGVbase using the BLAST algorithm to determine the positions of public SNPs. 4) For the exon module, cDNA/EST sequences are required that will be aligned to the genomic sequence using Spidey. 5) The data can be visualized in Ensembl's ContigView through a DAS annotation server and it requires SVG viewer to display all elements of the output page.
Weckx S, De Rijk P, Van Broeckhoven C, Del-Favero J. SNPbox: web-based high-throughput primer design from gene to genome. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W170-2. PubMed PMID: 15215373.
2004
100
Online
SNPdetector
http://lpg.nci.nih.go
Tool for automated identification of SNPs and mutations, which is helpful in the genome-scale research.
Zhang J, Wheeler DA, Yakub I, Wei S, Sood R, Rowe W, Liu PP, Gibbs RA, Buetow KH. SNPdetector: a software tool for sensitive and accurate SNP detection. PLoS Comput Biol. 2005 Oct;1(5):e53. Epub 2005 Oct 28. PubMed PMID: 16261194.
2005
100
Online
SNPexp
http://app3.titan.uio.no/biotools/tool.php?app=snpexp
Calculates and visualizes correlation between HapMap genotypes and gene expression levels.
Holm K, Melum E, Franke A, Karlsen TH. SNPexp - A web tool for calculating and visualizing correlation between HapMap genotypes and gene expression levels. BMC Bioinformatics. 2010 Dec 17;11:600. PubMed PMID: 21167019.
2010
100
Online
SNP-Flankplus
http://bio.kuas.edu.tw/snp-flankplus/
Retrieves SNP flanking sequences from the dbSNP and nucleotide databases of NCBI, which can be useful to design PCR primers for the SNP genotyping methods.
Yang CH, Cheng YH, Chuang LY, Chang HW. SNP-Flankplus: SNP ID-centric retrieval for SNP flanking sequences. Bioinformation. 2008;3(4):147-9. Epub 2008 Dec 6. PubMed PMID: 19238236.
2008
100
Online
SNPforID browser
http://spsmart.cesga.es/help.php?dataSets[]=snpforid52
Information on population based SNP genotype data and summarizing all that information into the most common population genetics indices such as allele frequencies, heterozygosity, etc.
Amigo J, Phillips C, Lareu M, Carracedo A. The SNPforID browser: an online tool for query and display of frequency data from the SNPforID project. Int J Legal Med. 2008 Sep;122(5):435-40. Epub 2008 May 20. PubMed PMID: 18491122.
2008
100
URL not working (as on 30 Nov 2013)
SNPHarvester
http://bioinformatics.ust.hk/SNPHarvester.html
Detects SNP-SNP interactions in GWA studies and serves to be useful in practical disease prognosis.
Yang C, He Z, Wan X, Yang Q, Xue H, Yu W. SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies. Bioinformatics. 2009 Feb 15;25(4):504-11. Epub 2008 Dec 19. PubMed PMID: 19098029.
2009
100
Online
SNPHunter
http://www.hsph.harvard.edu/ppg/software.htm
Software provides retrieval of SNP information and automatic SNP selection based on their physical position, function class and flanking sequences at user-defined lengths.
Niu T. SNPHunter: a versatile web-based tool for acquiring and managing single nucleotide polymorphisms. Methods Mol Biol. 2007;396:359-69. PubMed PMID: 18025704.
2007
100
Freely downloadable. Page not opening (as on 15 Nov 2013)
SNPinfo
http://snpinfo.niehs.nih.gov/
Xu Z, Taylor JA. SNPinfo: integrating GWAS and candidate gene information into functional SNP selection for genetic association studies. Nucleic Acids Res. 2009 Jul 1;37(Web Server issue):W600-5. Epub 2009 May 5. PubMed PMID: 19417063.
2009
100
Freely downloadable
SNPit
not available
Provides functional annotation information on SNPs, which is important in understanding the genome-wide association studies.
Shen TH, Carlson CS, Tarczy-Hornoch P. SNPit: a federated data integration system for the purpose of functional SNP annotation. Comput Methods Programs Biomed. 2009 Aug;95(2):181-9. Epub 2009 Mar 26. PubMed PMID: 19327864.
2009
100
Online
Identifies the chromosomal regions shared by family members by using the high density SNP genotype data and handles "tree pedigrees", which is useful to locate the shared chromosomal region(s), where the disease responsible gene(s) might reside.
Webb EL, Sellick GS, Houlston RS. SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal. Bioinformatics. 2005 Jul 1;21(13):3060-1. Epub 2005 Apr 19. PubMed PMID: 15840706.
2005
100
-
SNPmasker
http://bioinfo.ebc.ee/snpmasker/
Used for masking SNPs and repeats within the genome before primer and probe designing.
Andreson R, Puurand T, Remm M. SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes. Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W651-5. PubMed PMID: 16845091.
2006
100
Freely downloadable
SNPNB
http://bioinfo.vipbg.vcu.edu/SNPNB/
Efficiently handles genome-wide or chromosome-wide SNP data analysis and provides visualization of the bias patterns for SNPs or each type of SNPs.
Zhang F, Zhao Z. SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs). Bioinformatics. 2005 May 15;21(10):2517-9. Epub 2005 Mar 15. PubMed PMID: 15769840.
2005
100
Online. URL not working (as on 15 Nov 2013)
SNP-o-matic
http://snpomatic.sourceforge.net/
Provides a list of found known SNPs (either reference or alternate allele) while analyzing Solexa reads and comparing them to a reference so, it serves as a Solexa-based genotyping application.
Manske HM, Kwiatkowski DP. SNP-o-matic. Bioinformatics. 2009 Sep 15;25(18):2434-5. Epub 2009 Jul 2. PubMed PMID: 19574284.
2009
100
URL not working (as on 30 Nov 2013)
SNPosition
NOT AVAILABLE
Not available
Not available
100
Freely downloadable
SNPpy
NOT AVAILABLE
Not available
Not available
100
-
SNPrank
http://insilico.utulsa.edu/snprank/
1) It ranks the importance of single nucleotide polymorphisms (SNPs) in a genetic association interaction network (GAIN). 2) Each SNP is ranked according to its contribution to phenotype, including its main effect and second- and higher-order gene-gene interactions.
Davis NA, Pandey A, McKinney BA. Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS. Bioinformatics. 2011 Jan 15;27(2):284-5. Epub 2010 Nov 25. PubMed PMID: 21115438.
2011
100
-
SNPseek
http://snp.wustl.edu/cgi-bin/SNPseek/index.cgi
Information on human SNPs, frequencies, and annotation data.
Not available
Not available
100
Online
SNPselector
http://primer.duhs.duke.edu/
It searches the Ensembl genes or genomic regions (taken as input) for available SNPs and prioritizes these SNPs based on their tagging for linkage disequilibrium, allele frequencies and source, function, regulatory potential and repeat status.
SNPselector: a web tool for selecting SNPs for genetic association studies. Xu H, Gregory SG, Hauser ER, Stenger JE, Pericak-Vance MA, Vance JM, Züchner S, Hauser MA. Bioinformatics. 2005 Nov 15;21(22):4181-6. Epub 2005 Sep 22. PMID:16179360
2005
100
Online. Website mentions- 'Page is retired from public domain' (as on 11 Nov 2013)
SNPServer
http://hornbill.cspp.latrobe.edu.au/snpdiscovery.html
Uses BLAST to discover SNPs within DNA sequence data.
Savage D, Batley J, Erwin T, Logan E, Love CG, Lim GA, Mongin E, Barker G, Spangenberg GC, Edwards D. SNPServer: a real-time SNP discovery tool. Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W493-5. PubMed PMID: 15980519.
2005
100
URL not working (as on 11 Nov 2013)
SNPsetter
http://dna.leeds.ac.uk/snpsetter/
Provides details on standardization of SNP data.
Carr IM, Sheridan E, Hayward BE, Markham AF, Bonthron DT. IBDfinder and SNPsetter: tools for pedigree-independent identification of autozygous regions in individuals with recessive inherited disease. Hum Mutat. 2009 Jun;30(6):960-7. PubMed PMID: 19405095.
2009
100
Freely downloadable
SNPsFinder
http://snpsfinder.lanl.gov/
Facilitates the discovery of SNPs among closely related microorganisms.
Song J, Xu Y, White S, Miller KW, Wolinsky M. SNPsFinder--a web-based application for genome-wide discovery of single nucleotide polymorphisms in microbial genomes. Bioinformatics. 2005 May 1;21(9):2083-4. Epub 2005 Feb 3. PubMed PMID: 15691853.
2005
100
Freely downloadable
SNPSplicer
http://www.ikmb.uni-kiel.de/snpsplicer/
Investigates the effects of SNPs on splicing
ElSharawy A, Manaster C, Teuber M, Rosenstiel P, Kwiatkowski R, Huse K, Platzer M, Becker A, Nürnberg P, Schreiber S, Hampe J. SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs. Hum Mutat. 2006 Nov;27(11):1129-34. PubMed PMID: 16937379.
2006
100
Online
MicroSNiPer
http://cbdb.nimh.nih.gov/microsniper
Predicts the impact of SNP on microRNA binding site and provides graphical representation of the results.
Barenboim M, Zoltick BJ, Guo Y, Weinberger DR. MicroSNiPer: a web tool for prediction of SNP effects on putative microRNA targets. Hum Mutat. 2010 Nov;31(11):1223-32. doi: 10.1002/humu.21349. Epub 2010 Oct 7. PubMed PMID: 20809528.
2010
100
Online
SNPtoGO
https://webtools.imbs.uni-luebeck.de/snptogo/
Provides characterization of SNPs based on Gene Ontology (GO) terms.
Schwarz DF, Hädicke O, Erdmann J, Ziegler A, Bayer D, Möller S. SNPtoGO: characterizing SNPs by enriched GO terms. Bioinformatics. 2008 Jan 1;24(1):146-8. Epub 2007 Nov 17. PubMed PMID: 18024970.
2008
100
Freely downloadable. URL not working (as on 11 Nov 2013)
SNPTools
http://www.birc.au.dk/snptools
Provides analysis and visualization of microarray data, mainly SNP array data.
Sorensen FJ, Andersen CL, Wiuf C. SNPTools: a software tool for visualization and analysis of microarray data. Bioinformatics. 2007 Jun 15;23(12):1550-2. Epub 2007 Mar 24. PubMed PMID: 17384422.
2007
100
URL not working (as on 11 Nov 2013)
SNP-VISTA
http://genome.lbl.gov/vista/snpvista
Serves as a visualization tool. It provides: 1) mapping of SNPs to gene structure; 2) classification of SNPs, based on their location in the gene, frequency of occurrence in samples and allele composition; 3) clustering is done based on user-defined subsets of SNPs, highlighting haplotypes as well as recombinant sequences.
Shah N, Teplitsky MV, Minovitsky S, Pennacchio LA, Hugenholtz P, Hamann B, Dubchak IL. SNP-VISTA: an interactive SNP visualization tool. BMC Bioinformatics. 2005 Dec 8;6:292. PubMed PMID: 16336665.
2005
100
Online & freely downloadable
SOP3
http://biodev.hgen.pitt.edu/SOP3/
A tool for designing oligonucleotide primers, which are used for analysis of SNPs within the genome.
Alexander AM, Pecoraro C, Styche A, Rudert WA, Benos PV, Ringquist S, Trucco M. SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing. Biotechniques. 2005 Jan;38(1):87-94. PubMed PMID: 15679090.
2005
100
Page not opening (as on 11 Nov 2013)
SPOT - SNP prioritization online tool
https://spot.cgsmd.isi.edu/submit.php
Saccone SF, Bolze R, Thomas P, Quan J, Mehta G, Deelman E, Tischfield JA, Rice JP. SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W201-9. Epub 2010 Jun 6. PubMed PMID: 20529875.
2010
100
Online
StSNP - Structure SNP
http://ilyinlab.org/StSNP/
Compares the structural non- synonymous SNP distributions in many proteins or protein complexes.
Uzun A, Leslin CM, Abyzov A, Ilyin V. Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W384-92. Epub 2007 May 30. PubMed PMID: 17537826.
2007
100
Online
Sumstat
http://www.well.ox.ac.uk/gs2/
Manuscript under preparation as displayed on website.
Not available
100
Freely downloadable. URL not working (as on 11 Nov 2013)
S2G - Syndrome to gene
http://fohs.bgu.ac.il/s2g/index.html
1) Efficient tool to diagnose candidate genes for human diseases. 2) For linkage studies, it helps in finding related genes by using a query set of genes with the ability of choosing an area of the genome (using genes, SNP's or chromosome and physical location).
Gefen A, Cohen R, Birk OS. Syndrome to gene (S2G): in-silico identification of candidate genes for human diseases. Hum Mutat. 2010 Mar;31(3):229-36. PubMed PMID: 20052752.
2010
100
Online
Synthesis-View
http://chgr.mc.vanderbilt.edu/ritchielab/method.php?method=synthesisview
A visualization tool, which plots information on SNP genomic locations, presence of the SNP in a specific study or analysis, as well as related data such as genetic effect size and summary phenotype information, according to user preferences.
Pendergrass SA, Dudek SM, Crawford DC, Ritchie MD. Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis. BioData Min. 2010 Dec 16;3:10. PubMed PMID: 21162740.
2010
100
Online
TAGster
http://www.niehs.nih.gov/research/resources/software/tagster/
It selects, evaluates and visualizes LD tag SNPs both for single and multiple populations.
Xu Z, Kaplan NL, Taylor JA. TAGster: efficient selection of LD tag SNPs in single or multiple populations. Bioinformatics. 2007 Dec 1;23(23):3254-5. Epub 2007 Sep 7. PubMed PMID: 17827206.
2007
100
Freely downloadable. URL not working (as on 7 Nov 2013).
The SNP ratio test
http://sourceforge.net/projects/snpratiotest/
The SNP ratio test is used to assess significant associations in genome-wide association studies.
O'Dushlaine C, Kenny E, Heron EA, Segurado R, Gill M, Morris DW, Corvin A. The SNP ratio test: pathway analysis of genome-wide association datasets. Bioinformatics. 2009 Oct 15;25(20):2762-3. Epub 2009 Jul 20. PubMed PMID: 19620097.
2009
100
Freely downloadable
UTRscan
http://itbtools.ba.itb.cnr.it/utrscan
Computes SNPs in the 5 2 and 3 2 untranslated regions.
Not available
Not available
100
VarDetect
http://www4a.biotec.or.th/GI/tools/vardetect
It is a sequence variation exploration tool, which automatically detects nucleotide variation from fluorescence based chromatogram traces.
Ngamphiw C, Kulawonganunchai S, Assawamakin A, Jenwitheesuk E, Tongsima S. VarDetect: a nucleotide sequence variation exploratory tool. BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S9. PubMed PMID: 19091032.
2008
100
Freely downloadable
Variant Name Mapper
http://www.hugenavigator.net/HuGENavigator/startPageMapper.do
Maps gene variant common names to their corresponding rs numbers, which is compiled from web sources like SNPedia, SNP500 cancer, ALFRED, HuGE Navigator, OMIM, etc.
Yu W, Ned R, Wulf A, Liu T, Khoury MJ, Gwinn M. The need for genetic variant naming standards in published abstracts of human genetic association studies. BMC Res Notes. 2009 Apr 14;2:56. doi: 10.1186/1756-0500-2-56. PubMed PMID: 19366450; PubMed Central PMCID: PMC2672936
2009
100
Online
varLD
http://www.nus-cme.org.sg/software/varld.html
A program, which quantifies variation in linkage disequilibrium patterns between populations (Chinese, Malays and Indians).
Ong RT, Teo YY. varLD: a program for quantifying variation in linkage disequilibrium patterns between populations. Bioinformatics. 2010 May 1;26(9):1269-70. Epub 2010 Mar 22. PubMed PMID: 20308177.
2010
100
Freely downloadable
viewGene
http://chakravarti.som.jhmi.edu/viewGene/viewGene.html
A useful tool to aid in the visualization and characterization of sequence and polymorphism data.
Kashuk C, SenGupta S, Eichler E, Chakravarti A. ViewGene: a graphical tool for polymorphism visualization and characterization. Genome Res. 2002 Feb;12(2):333-8. PubMed PMID: 11827953.
2002
100
URL not working (as on 7 Nov 2013)
WASP - Web-based Allele-Specific Primer designing tool
http://bioinfo.biotec.or.th/WASP
Designs allele-specific (AS) primers for detecting SNPs and mutations.
Wangkumhang P, Chaichoompu K, Ngamphiw C, Ruangrit U, Chanprasert J, Assawamakin A, Tongsima S. WASP: a Web-based Allele-Specific PCR assay designing tool for detecting SNPs and mutations. BMC Genomics. 2007 Aug 14;8:275. PubMed PMID: 17697334.
2007
100
Online
WatCut
http://watcut.uwaterloo.ca/watcut/watcut/template.php
An online tool for SNP-RFLP analysis, which detects single nucleotide polymorphisms by introducing restriction sites that will cleave only one variant sequence.
Not available
Not available
100
Online
A cSNP Map and Database for Human Chromosome 21
http://csnp.unige.ch/
Provides details on the SNPs within the cDNA sequences of human chromosome 21
Deutsch S, Iseli C, Bucher P, Antonarakis SE, Scott HS. A cSNP map and database for human chromosome 21. Genome Res. 2001 Feb;11(2):300-7. PubMed PMID: 11157793
2001
100
Online
A SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua)
NOT AVAILABLE
An extensive resource of SNP markers for Atlantic cod, Gadus morhua.
Hubert S, Higgins B, Borza T, Bowman S. Development of a SNP resource and a genetic linkage map for Atlantic cod (Gadus morhua). BMC Genomics. 2010 Mar 22;11:191. PubMed PMID: 20307277
2010
100
-
A SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)
NOT AVAILABLE
Information on SNPs in Pacific white shrimp (Litopenaeus vannamei).
Ciobanu DC, Bastiaansen JW, Magrin J, Rocha JL, Jiang DH, Yu N, Geiger B, Deeb N, Rocha D, Gong H, Kinghorn BP, Plastow GS, van der Steen HA, Mileham AJ. A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Anim Genet. 2010 Feb;41(1):39-47. Epub 2009 Oct 2. PubMed PMID: 19799596.
2010
100
-
AutoSNPdb
http://autosnpdb.qfab.org.au/
Provides information on SNPs present in crop plants like barley, brassica, wheat and rice.
Duran C, Appleby N, Clark T, Wood D, Imelfort M, Batley J, Edwards D. AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants. Nucleic Acids Res. 2009 Jan;37(Database issue):D951-3. Epub 2008 Oct 14. PubMed PMID: 18854357; PubMed Central PMCID: PMC2686484.
2009
100
Online
BcSNPdb
http://snugenome.snu.ac.kr/BtcSNP/
Provides information on bovine coding SNPs
Moon S, Shin HD, Cheong HS, Cho HY, Namgoong S, Kim EM, Han CS, Sung S, Kim H. BcSNPdb: bovine coding region single nucleotide polymorphisms located proximal to quantitative trait loci. J Biochem Mol Biol. 2007 Jan 31;40(1):95-9. PubMed PMID: 17244488.
2007
100
Online
Bovine in silico SNP (IBISS) database
http://www.livestockgenomics.csiro.au/cow/
An interactive database of bovine ESTs, which shows putative SNPs, model bovine mRNAs, and their relation to both the human genome and bovine reference mRNA and protein sequences.
Hawken RJ, Barris WC, McWilliam SM, Dalrymple BP. An interactive bovine in silico SNP database (IBISS). Mamm Genome. 2004 Oct;15(10):819-27. PubMed PMID: 15520884.
2004
100
Online
CaSNP
http://cistrome.dfci.harvard.edu/CaSNP/
A collection of copy number alteration (CNA) from SNP arrays of 34 different cancer types.
Cao Q, Zhou M, Wang X, Meyer CA, Zhang Y, Chen Z, Li C, Liu XS. CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. Nucleic Acids Res. 2011 Jan;39(Database issue):D968-74. Epub 2010 Oct 23. PubMed PMID: 20972221.
2011
100
Online
CGDSNPdb
http://cgd.jax.org/cgdsnpdb/
Provides information on more than 66 million SNPs from 136 strains of laboratory mice and also integrates the SNP data with nearby gene annotations, including crosslinks, using Ensembl and MGI annotations.
Hutchins LN, Ding Y, Szatkiewicz JP, Von Smith R, Yang H, de Villena FP, Churchill GA, Graber JH. CGDSNPdb: a database resource for error-checked and imputed mouse SNPs. Database (Oxford). 2010 Jul 6;2010:baq008. Print 2010. PubMed PMID: 20624716.
2010
100
Online
CNVVdb
http://cnvvdb.genomics.sinica.edu.tw/
Chen FC, Chen YZ, Chuang TJ. CNVVdb: a database of copy number variations across vertebrate genomes. Bioinformatics. 2009 Jun 1;25(11):1419-21. Epub 2009 Mar 25. PubMed PMID: 19321736.
2009
100
Online. URL not working as on 30 October 2013.
dbDNV
http://goods.ibms.sinica.edu.tw/DNVs/
Provides information on SNPs coupled with duplicated-gene nucleotide variants (DNVs) within the human genome.
Ho MR, Tsai KW, Chen CH, Lin WC. dbDNV: a resource of duplicated gene nucleotide variants in human genome. Nucleic Acids Res. 2011 Jan;39(Database issue):D920-5. Epub 2010 Nov 21. PubMed PMID: 21097891.
2011
100
Online
dbSMR
http://miracle.igib.res.in/dbSMR
Provides information on the SNPs in and around predicted miRNA target sites within the human genome.
Hariharan M, Scaria V, Brahmachari SK. dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation. BMC Bioinformatics. 2009 Apr 16;10:108. PubMed PMID: 19371411.
2009
100
Online. URL not working (as on 30 October 2013).
DPDB - Drosophila polymorphism database
http://dpdb.uab.es/dpdb/dpdb.asp
Provides a collection of all the existing polymorphic sequences in the Drosophila genus.
Casillas S, Petit N, Barbadilla A. DPDB: a database for the storage, representation and analysis of polymorphism in the Drosophila genus. Bioinformatics. 2005 Sep 1;21 Suppl 2:ii26-30. PubMed PMID: 16204116
2005
100
-
FLYSNPdb
http://flysnp.imp.ac.at/flysnpdb.php
Provides a genome-wide map of single nucleotide polymorphisms present in the Drosophila genome.
Chen D, Berger J, Fellner M, Suzuki T. FLYSNPdb: a high-density SNP database of Drosophila melanogaster. Nucleic Acids Res. 2009 Jan;37(Database issue):D567-70. Epub 2008 Sep 10. PubMed PMID: 18784187.
2009
100
Online
FESD - Functional Element SNPs Database
http://sysbio.kribb.re.kr:8080/fesd/index.jsp
Information on SNPs present in the specific functional elements (such as promoter regions, CpG islands, 5'-untranslated regions (5'-UTRs), translation start sites, splice sites, coding exons, introns, etc.) of the human genic regions.
Kang HJ, Choi KO, Kim BD, Kim S, Kim YJ. FESD: a Functional Element SNPs Database in human. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D518-22. Erratum in: Nucleic Acids Res. 2005;33(1):449. PubMed PMID: 15608252.
2005
100
Online. URL not working (as on 29 October 2013).
FunctSNP
http://functsnp.sourceforge.net/index.html
FunctSNP provides a unified bioinformatics resource to link SNPs with functional knowledge (e.g., genes, pathways, ontologies).
Goodswen SJ, Gondro C, Watson-Haigh NS, Kadarmideen HN. FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases. BMC Bioinformatics. 2010 Jun 9;11:311. PubMed PMID: 20534127.
2010
100
-
GEAD & JG-SNP
http://www.tmghig.jp/jg-snp/english/E_top.html
Provides information on the role of genetic polymorphism (single nucleotide polymorphism) in the development of geriatric disease among the Japanese population.
Sawabe M, Arai T, Kasahara I, Esaki Y, Nakahara K, Hosoi T, Orimo H, Takubo K, Murayama S, Tanaka N; Tokyo Metropolitan Geriatric Medical Center; Japan Science and Technology Agency. Developments of geriatric autopsy database and Internet-based database of Japanese single nucleotide polymorphisms for geriatric research (JG-SNP). Mech Ageing Dev. 2004 Aug;125(8):547-52. PubMed PMID: 15336912.
2004
100
Online
Genevar
http://www.sanger.ac.uk/resources/software/genevar/
It is a platform of database and web services designed for data integration, analysis and visualization of SNP-gene associations in eQTL (expression quantitative trait loci) studies.
Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, Stranger BE, Deloukas P, Dermitzakis ET. Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics. 2010 Oct 1;26(19):2474-6. Epub 2010 Aug 10. PubMed PMID: 20702402.
2010
100
Freely downloadable
Go!Poly
http://61.139.84.5/gopoly/
Provides access to gene-related variation data in human.
Zhang G, Zhang S, Chen W, Qiu W, Wu H, Wang J, Luo J, Gu X, Cotton RG. Go!Poly: A gene-oriented polymorphism database. Hum Mutat. 2001 Nov;18(5):382-7. PubMed PMID: 11668631.
2001
100
URL not working (as on 29 Oct 2013)
GoSh
http://www.itb.cnr.it/gosh/snps.php
Provides detailed information on SNPs found in the goat and sheep genome.
Caprera A, Lazzari B, Stella A, Merelli I, Caetano AR, Mariani P. GoSh: a web-based database for goat and sheep EST sequences. Bioinformatics. 2007 Apr 15;23(8):1043-5. Epub 2007 Mar 24. PubMed PMID: 17384426.
2007
100
Online
GWAS Analyzer
http://nwrce.org/gwas-analyzer
Provides access to the data from a genome-wide association study of human susceptibility to bacterial infection.
Fong C, Ko DC, Wasnick M, Radey M, Miller SI, Brittnacher M. GWAS analyzer: integrating genotype, phenotype and public annotation data for genome-wide association study analysis. Bioinformatics. 2010 Feb 15;26(4):560-4. Epub 2010 Jan 6. PubMed PMID: 20053839.
2010
100
Online
HGBASE - Human Genic Bi-Allelic Sequences
http://hgbase.cgr.ki.se
A database of SNPs and other variations in and around the human genes.
Brookes AJ. HGBASE--a unified human SNP database. Trends Genet. 2001 Apr;17(4):229. PubMed PMID: 11357826.
2001
100
URL not working (as on 29 Oct 2013)
HLungDB
http://www.megabionet.org/bio/hlung
Incorporates information on the transcription factor binding motifs, the promoters, the SNP sites for each genes, as well as related clinical information and experiment evidences in context to lung cancer.
Wang L, Xiong Y, Sun Y, Fang Z, Li L, Ji H, Shi T. HLungDB: an integrated database of human lung cancer research. Nucleic Acids Res. 2010 Jan;38(Database issue):D665-9. Epub 2009 Nov 9. PubMed PMID: 19900972.
2010
100
SNP view' section not responsing as on 28 Oct 2013
HSPVdb - Human Short Peptide Variation Database
http://srs.bioinformatics.nl/hspv/
1) Provides information on peptide variation arising due single nucleotide polymorphisms (SNPs). 2) Constructed mainly with the purpose of finding human T cell epitopes and identifying minor histocompatibility antigens (mHags) in combination with mass spectrometry.
Nijveen H, Kester MG, Hassan C, Viars A, de Ru AH, de Jager M, Falkenburg JH, Leunissen JA, van Veelen PA. HSPVdb--the Human Short Peptide Variation Database for improved mass spectrometry-based detection of polymorphic HLA-ligands. Immunogenetics. 2011 Mar;63(3):143-53. Epub 2010 Dec 2. PubMed PMID: 21125265.
2011
100
Online
IVDB - Influenza Virus Database
http://influenza.big.ac.cn/
Provides a series of tools and viewers for analyzing the viral genomes, genes, genetic polymorphisms and phylogenetic relationships comparatively. Also, presents the results by SNP distribution plots and minor allele distributions.
Chang S, Zhang J, Liao X, Zhu X, Wang D, Zhu J, Feng T, Zhu B, Gao GF, Wang J, Yang H, Yu J, Wang J. Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research. Nucleic Acids Res. 2007 Jan;35(Database issue):D376-80. Epub 2006 Oct 25. PubMed PMID: 17065465.
2007
100
Online
KAIKObase
http://sgp.dna.affrc.go.jp/KAIKObase/index.html?keyword-and-position-search
An integrated silkworm genome database and can provide information on the SNP markers.
Shimomura M, Minami H, Suetsugu Y, Ohyanagi H, Satoh C, Antonio B, Nagamura Y, Kadono-Okuda K, Kajiwara H, Sezutsu H, Nagaraju J, Goldsmith MR, Xia Q, Yamamoto K, Mita K. KAIKObase: an integrated silkworm genome database and data mining tool. BMC Genomics. 2009 Oct 21;10:486. PubMed PMID: 19843344.
2009
100
Online
LSMDB - Locus Specific Mutation Databases
http://www.genomic.unimelb.edu.au/mdi/dblist/glsdb.html
Claustres M, Horaitis O, Vanevski M, Cotton RG. Time for a unified system of mutation description and reporting: a review of locus-specific mutation databases. Genome Res. 2002 May;12(5):680-8. PMID:11997335
2002
100
Online
MamPol
http://mampol.uab.es/
Provides information on all the existing polymorphic sequences in the Mammalia group.
Egea R, Casillas S, Fernández E, Senar MA, Barbadilla A. MamPol: a database of nucleotide polymorphism in the Mammalia class. Nucleic Acids Res. 2007 Jan;35(Database issue):D624-9. Epub 2006 Nov 16. PMID:17142236
2007
100
Online
MamuSNP
http://mamusnp.ucdavis.edu/query.php
Identifies SNPs, which are widely distributed throughout the coding and non-coding regions of a Macaca mulatta genome.
Malhi RS, Sickler B, Lin D, Satkoski J, Tito RY, George D, Kanthaswamy S, Smith DG. MamuSNP: a resource for Rhesus Macaque (Macaca mulatta) genomics. PLoS One. 2007 May 9;2(5):e438. PubMed PMID: 17487284.
2007
100
Freely downloadable
miRGen 2.0
http://diana.cslab.ece.ntua.gr/mirgen/
Provides information about the position of human and mouse microRNA coding transcripts and also details on the Single nucleotide polymorphisms associated with microRNAs.
Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M, Grosse I, Sellis T, Hatzigeorgiou AG. miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res. 2010 Jan;38(Database issue):D137-41. Epub 2009 Oct 22. PubMed PMID: 19850714.
2010
100
Online
MitoVariome
http://variome.kobic.re.kr/MitoVariome/
Provides information on the genetic variation in the human mitochondrial genome along with graphical view.
Lee YS, Kim WY, Ji M, Kim JH, Bhak J. MitoVariome: a variome database of human mitochondrial DNA. BMC Genomics. 2009 Dec 3;10 Suppl 3:S12. PMID:19958475
2009
100
Online
MonkeySNP
http://monkeysnp.ohsu.edu/snp/ OR http://monkeysnp.ohsu.edu/snp/index.jsp
Khouangsathiene S, Pearson C, Street S, Ferguson B, Dubay C. MonkeySNP: a web portal for non-human primate single nucleotide polymorphisms. Bioinformatics. 2008 Nov 15;24(22):2645-6. Epub 2008 Sep 16. PubMed PMID: 18796476
2008
100
Online
NordicDB
http://www.nordicdb.org/database/Home.html
Provides information about the genome-wide association study (GWAS) data samples and details on how to access both the directly genotyped and imputed data.
Leu M, Humphreys K, Surakka I, Rehnberg E, Muilu J, Rosenstrom P, Almgren P, Jaaskelainen J, Lifton RP, Kyvik KO, Kaprio J, Pedersen NL, Palotie A, Hall P, Gronberg H, Groop L, Peltonen L, Palmgren J, Ripatti S. NordicDB: a Nordic pool and portal for genome-wide control data. Eur J Hum Genet. 2010 Dec;18(12):1322-6. Epub 2010 Jul 28. PubMed PMID: 20664631.
2010
100
Data can be downloaded
ORFDB
http://orf.invitrogen.com/
Provides a highly flexible technology (SNP genotyping assays kits) for detection of polymorphism within any genome.
Liang F, Matrubutham U, Parvizi B, Yen J, Duan D, Mirchandani J, Hashima S, Nguyen U, Ubil E, Loewenheim J, Yu X, Sipes S, Williams W, Wang L, Bennett R, Carrino J. ORFDB: an information resource linking scientific content to a high-quality Open Reading Frame (ORF) collection. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D595-9. PubMed PMID: 14681490.
2004
100
Online
Patrocles
http://www.patrocles.org/MyPatrocles.php
Hiard S, Charlier C, Coppieters W, Georges M, Baurain D. Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates. Nucleic Acids Res. 2010 Jan;38(Database issue):D640-51. Epub 2009 Nov 11. PubMed PMID: 19906729.
2010
100
Online
PDA - Pooled DNA Analyzer
http://www.ibms.sinica.edu.tw/%7Ecsjfann/first%20flow/pda.htm
Software for the anlysis of pooled DNA data for association studies to identify disease susceptibility genes.
Yang HC, Pan CC, Lin CY, Fann CS. PDA: Pooled DNA analyzer. BMC Bioinformatics. 2006 Apr 28;7:233. PubMed PMID: 16643673.
2006
100
Online
PEPPI - PEPtidomics Protein Isoform Database
http://discern.uits.iu.edu:8340/peppi/index.php
Information on SNPs within the protein isoforms.
Zhou A, Zhang F, Chen JY. PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S7. PubMed PMID: 20946618.
2010
100
Online
PhD-SNP - Predictor of human Deleterious Single Nucleotide Polymorphisms
http://gpcr2.biocomp.unibo.it/cgi/predictors/PhD-SNP/PhD-SNP.cgi
Provides information on the mutant position present in the protein sequences to predict the deleterious SNPs.
Capriotti E, Calabrese R, Casadio R. Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information. Bioinformatics. 2006 Nov 15;22(22):2729-34. Epub 2006 Aug 7. PubMed PMID: 16895930.
2006
100
Online
PmiRKB
http://bis.zju.edu.cn/pmirkb/
Detects SNPs in the pre-miRNAs and miRNAs of two model plants- Arabidopsis and Rice.
Meng Y, Gou L, Chen D, Mao C, Jin Y, Wu P, Chen M. PmiRKB: a plant microRNA knowledge base. Nucleic Acids Res. 2011 Jan;39(Database issue):D181-7. Epub 2010 Aug 18. PubMed PMID: 20719744.
2011
100
Online
PoMaMo - Potato Maps and More database
http://www.gabipd.org/projects/Pomamo/
Provides information on sequences, mapping, SNPs etc. of potato plant.
Meyer S, Nagel A, Gebhardt C. PoMaMo--a comprehensive database for potato genome data. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D666-70. PubMed PMID: 15608284.
2005
100
Online
ProbABEL
http://www.genabel.org/manuals/ProbABEL
Uses statistical approach to relate SNP information with genome-wide association studies.
Aulchenko YS, Struchalin MV, van Duijn CM. ProbABEL package for genome-wide association analysis of imputed data. BMC Bioinformatics. 2010 Mar 16;11:134. PubMed PMID: 20233392.
2010
100
Files for execution available
rSNP_Guide
http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/
1) Comprises of 4 sub-databases cross-linked to each other (rSNP_DB, rSNP_BIB, SYSTEM and rSNP_Report. 2) Documents the influence of SNPs in the regulatory gene regions and onto DNA interactions with nuclear proteins.
Ponomarenko JV, Merkulova TI, Orlova GV, Fokin ON, Gorshkova EV, Frolov AS, Valuev VP, Ponomarenko MP. rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation. Nucleic Acids Res. 2003 Jan 1;31(1):118-21. PubMed PMID: 12519962.
2003
100
Online
SCAN - SNP and Copy number Annotation
http://www.scandb.org/newinterface/about.html
Provides both physical and funtional annotation of SNPs.
Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL, Dolan ME, Cox NJ. SCAN: SNP and copy number annotation. Bioinformatics. 2010 Jan 15;26(2):259-62. Epub 2009 Nov 17. PubMed PMID: 19933162
2010
100
Online
SNP Function Portal
http://brainarray.mbni.med.umich.edu/Brainarray/Database/SearchSNP/ snpfunc.aspx
Provides SNP functional annotations in six major categories including genomic elements, transcription regulation, protein function, pathway, disease and population genetics.
Wang P, Dai M, Xuan W, McEachin RC, Jackson AU, Scott LJ, Athey B, Watson SJ, Meng F. SNP Function Portal: a web database for exploring the function implication of SNP alleles. Bioinformatics. 2006 Jul 15;22(14):e523-9. PubMed PMID: 16873516.
2006
100
Online
SNP resource for Pacific white shrimp (Litopenaeus vannamei)
NOT AVAILABLE
SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)
Ciobanu DC, Bastiaansen JW, Magrin J, Rocha JL, Jiang DH, Yu N, Geiger B, Deeb N, Rocha D, Gong H, Kinghorn BP, Plastow GS, van der Steen HA, Mileham AJ. A major SNP resource for dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei). Anim Genet. 2010 Feb;41(1):39-47. Epub 2009 Oct 2. PubMed PMID: 19799596.
2010
100
-
SNP Resource for Human Chromosome 22
NOT AVAILABLE
Reports the dentification and characterization of 12,267 potential variants (SNPs and other small insertions/deletions) of human chromosome 22.
Dawson E, Chen Y, Hunt S, Smink LJ, Hunt A, Rice K, Livingston S, Bumpstead S, Bruskiewich R, Sham P, Ganske R, Adams M, Kawasaki K, Shimizu N, Minoshima S, Roe B, Bentley D, Dunham I. A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence. Genome Res. 2001 Jan;11(1):170-8. PubMed PMID: 11156626.
2001
100
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SNPExpress
http://www.planetmathematics.com/SNPExpress/
Provides an integrated view of both large scale SNP genotyping and gene expression.
Sanders MA, Verhaak RG, Geertsma-Kleinekoort WM, Abbas S, Horsman S, van der Spek PJ, Löwenberg B, Valk PJ. SNPExpress: integrated visualization of genome-wide genotypes, copy numbers and gene expression levels. BMC Genomics. 2008 Jan 25;9:41. PubMed PMID: 18221515.
2008
100
Freely downloadable. A computer with a memory of 1024MB is advised and it requires a runtime environment of JAVA 1.5 or higher.
SNPnexus
http://www.snp-nexus.org/
It s a SNP annotation tool, which helps in the selection of functionally relevant SNPs for large-scale genotyping studies. Allows single queries using dbSNP identifiers or chromosomal regions for annotating the known variants.
Chelala C, Khan A, Lemoine NR. SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms. Bioinformatics. 2009 Mar 1;25(5):655-61. Epub 2008 Dec 19. PubMed PMID: 19098027.
2009
100
Online
SNPSTR
http://www.sbg.bio.ic.ac.uk/~ino/
Information on compound genetic marker called SNPSTR which combines a microsatellite marker (STR) with one or more tightly linked SNPs and severs a great tool to study population genetics of all model organisms.
Agrafioti I, Stumpf MP. SNPSTR: a database of compound microsatellite-SNP markers. Nucleic Acids Res. 2007 Jan;35(Database issue):D71-5. PubMed PMID: 17202172.
2007
100
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SPSmart
http://spsmart.cesga.es/
Provides information on population based SNP data.
Amigo J, Salas A, Phillips C, Carracedo A. SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access. BMC Bioinformatics. 2008 Oct 10;9:428. PubMed PMID: 18847484.
2008
100
Files for execution available
ssSNPTarget
http://variome.kobic.re.kr/ ssSNPTarget/ or http://ssSNPTarget.org
Identifies splice-site SNPs distributed in human and mouse genes and their effects on transcripts and mouse.
Yang JO, Kim WY, Bhak J. ssSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database. Hum Mutat. 2009 Dec;30(12):E1010-20. PubMed PMID: 19760752.
2009
100
T2D-Db
http://t2ddb.ibab.ac.in/home.shtml
Provides SNP data for the candidate genes reported to be associated with Type2 diabetes.
Agrawal S, Dimitrova N, Nathan P, Udayakumar K, Lakshmi SS, Sriram S, Manjusha N, Sengupta U. T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. BMC Genomics. 2008 Jul 7;9:320. PubMed PMID: 18605991.
2008
100
Online
TAMAL
http://neoref.ils.unc.edu/tamal/
Provides information on SNPs for genetic studies of human complex traits.
Hemminger BM, Saelim B, Sullivan PF. TAMAL: an integrated approach to choosing SNPs for genetic studies of human complex traits. Bioinformatics. 2006 Mar 1;22(5):626-7. Epub 2006 Jan 17. PubMed PMID: 16418238.
2006
100
Online. URL not working as on 21 October 2013.
TcSNP
http://snps.tcruzi.org/
Provides information on the genetic variation of different strains of Trypanosoma cruzi
Ackermann AA, Carmona SJ, Agüero F. TcSNP: a database of genetic variation in Trypanosoma cruzi. Nucleic Acids Res. 2009 Jan;37(Database issue):D544-9. Epub 2008 Oct 30. PubMed PMID: 18974180.
2009
100
Online
The Bovine Genome Database
http://genomes.arc.georgetown.edu/bovine/index.shtml
Childers CP, Reese JT, Sundaram JP, Vile DC, Dickens CM, Childs KL, Salih H, Bennett AK, Hagen DE, Adelson DL, Elsik CG. Bovine Genome Database: integrated tools for genome annotation and discovery. Nucleic Acids Res. 2011 Jan;39(Database issue):D830-4. Epub 2010 Dec 1. PubMed PMID: 21123190.
2011
100
Online
The catfish genome database cBARBEL
http://catfishgenome.org/cbarbel/
Provides visualization of catfish linkage, physical and integrated maps, a catfish EST contig viewer with SNP information overlay.
Lu J, Peatman E, Yang Q, Wang S, Hu Z, Reecy J, Kucuktas H, Liu Z. The catfish genome database cBARBEL: an informatic platform for genome biology of ictalurid catfish. Nucleic Acids Res. 2011 Jan;39(Database issue):D815-21. Epub 2010 Oct 8. PubMed PMID: 20935046.
2011
100
Online. URL not working as on 21 October 2013
Definitive Haplotype Database (D-HaploDB)
http://orca.gen.kyushu-u.ac.jp/
Provides information on genome-wide definitive haplotypes, which are determined by genotyping complete hydatidiform mole samples from Japanese population.
Higasa K, Miyatake K, Kukita Y, Tahira T, Hayashi K. D-HaploDB: a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples. Nucleic Acids Res. 2007 Jan;35(Database issue):D685-9. Epub 2006 Dec 13. PubMed PMID: 17166862.
2007
100
Online
TOMATOMA
http://tomatoma.nbrp.jp/index.jsp
Provides information on the mutant seeds of tomato, which are generated by EMS treatment of gamma-ray irradiation.
TOMATOMA: a novel tomato mutant database distributing Micro-Tom mutant collections. Saito T, Ariizumi T, Okabe Y, Asamizu E, Hiwasa-Tanase K, Fukuda N, Mizoguchi T, Yamazaki Y, Aoki K, Ezura H. Plant Cell Physiol. 2011 Feb;52(2):283-96. Epub 2011 Jan 21.
2011
100
Online
topoSNP
http://gila.bioengr.uic.edu/snp/toposnp/
Provides information about the topographic mapping of the disease and non-disease associated non-synonymous SNPs.
Stitziel NO, Binkowski TA, Tseng YY, Kasif S, Liang J. topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D520-2. PubMed PMID: 14681472.
2004
100
Online. Requires freely available CHIME plug-in for 3D representation of the molecules.
Varietas
http://kokki.uku.fi/bioinformatics/varietas/
Paananen J, Ciszek R, Wong G. Varietas: a functional variation database portal. Database (Oxford). 2010 Jul 29;2010:baq016. Print 2010. PubMed PMID: 20671203.
2010
100
URL not working (as on 14 Sep 2013)
VarySysDB
http://h-invitational.jp/varygene/
Comprises of three systems- Genome browser, LD search and VaryGene2
VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. Shimada MK, Matsumoto R, Hayakawa Y, Sanbonmatsu R, Gough C, Yamaguchi-Kabata Y, Yamasaki C, Imanishi T, Gojobori T. Nucleic Acids Res. 2009 Jan;37(Database issue):D810-5.
2009
100
Online
VSD
www.chgb.org.cn/vsd.htm
1. Provides information on the varitation data, which is extracted from the publicly available databases. 2. Developed as a locus-specific resource to identify susceptible genes for shizophrenia.
Zhou M, Zhuang YL, Xu Q, Li YD, Shen Y. VSD: a database for schizophrenia candidate genes focusing on variations. Hum Mutat. 2004 Jan;23(1):1-7. PubMed PMID: 14695526.
2004
100
URL not working (as on 13 Sep 2013)
ThaiSNP-2
http://www4a.biotec.or.th/thaisnp2/
1) Uses the 5th generation Affymetrix SNP genotyping array to determine Single Nucleotide Polymorphisms (SNPs) and Copy Number Variations (CNVs) in Thai population. 2) It can search SNP information from gene, chromosome position, associated disease and SNP ID.
Not available in Pubmed
Not available
100
IGVdb
http://www.igvdb.res.in/index.php
1) Aims to discover SNPs, CNVs and repeats in over 1000 genes, which are biomedically important and also genes of pharmacogenetic relevance in the Indian population. 2) Use the haplotype maps for disease association studies and pharmacogenetics.
Indian Genome Variation Consortium. The Indian Genome Variation database (IGVdb): a project overview. Hum Genet. 2005 Oct;118(1):1-11. Epub 2005 Aug 25. Review. PubMed PMID: 16133172
2005
100
Requires online registration.
PredictSNP
http://loschmidt.chemi.muni.cz/predictsnp
1) Predicts the disease-related mutations by the analysis of single nucleotide variants in the coding regions and the effect of amino acid substitution. 2) Serves as a consensus classifier, which combines six of the top performing tools for the prediction of the effects of mutation on protein function and the obtained results are provided together with the annotations extracted from the Protein Mutant Database and the UniProt database.
Bendl J, Stourac J, Salanda O, Pavelka A, Wieben ED, Zendulka J, Brezovsky J and Damborsky J. PredictSNP: Robust and accurate consensus classifier for prediction of disease-related mutations. PLoS Comput Bi7ol. 2014 Jan; 10(1):e1003440. doi: 10.1371/journal.pcbi.1003440. Epub 2014 Jan 16. PubMed PMID: 24453961; PMCID: PMC3894168.
2014
100
Tool contributed to the portal by Jarsolav Bendl (one of the developers of the tool) on May 14, 2014
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