SNP analysis

Haploview
www.broad.mit.edu/mpg/haploview/

1) It provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data. 2) Basically it takes genotypic file(.ped file & .info file) as input & performs Ld plots for higly associated markers & other statistics for it & also gives haplotype blocks for highly associated markers & performs other complex statistics for it (association tests for the SNP markers). 3) Especially useful for Hapmap data if user wants to visualize it nicely.

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.

2004

Freely downloadable

dbSNP
http://www.ncbi.nlm.nih.gov/projects/SNP/

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

Online

HapMap
http://hapmap.ncbi.nlm.nih.gov/

International HapMap Consortium. The International HapMap Project. Nature. 2003 Dec 18;426(6968):789-96. PubMed PMID: 14685227.

Not available

Online

PolyPhen
http://polydoms.cchmc.org/polydoms/

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

Online

WormBase
http://www.wormbase.org/

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, M�ller 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

2009

Online

SIFT - Sorting Tolerant From Intolerant
http://bio.kuas.edu.tw/Seq-SNPing

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

DOES NOT WORK

HAP
not available

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

HMDB - Human Metabolome Database
http://www.hmdb.ca/

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

Online

BioMart
http://www.biomart.org/

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

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

DOES NOT WORK

PMUT
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

DOES NOT WORK

SNPSpD - SNP SPectral Decomposition
http://snpsfinder.lanl.gov/

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

Online

JSNP - Japanese Single Nucleotide Polymorphisms
http://snp.ims.u-tokyo.ac.jp/

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

Online

SNPper
http://snpper.chip.org/

Manske HM, Kwiatkowski DP. SNP-o-matic. Bioinformatics. 2009 Sep 15;25(18):2434-5. Epub 2009 Jul 2. PubMed PMID: 19574284.

2002

Online registration

ARTS
http://andromeda.gsf.de/arts

Klaften M, Hrab� 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

Online

DnaSP
http://www.ub.edu/dnasp

(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.

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

Freely downloadable

SNPs3D
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. input- .raw,.tab,.txt format & species-humans, python,matlab,java, CPU & GPU versions.

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

Online

Structure
http://pritch.bsd.uchicago.edu/structure.html

Not available

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

Online

ECR browser
http://ecrbrowser.dcode.org/

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

Online

PupaSuite
http://polly.wustl.edu/promolign/main.html

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

DOES NOT WORK

SLOPE
http://www.math.hkbu.edu.hk/~mng/SKM-SNP/SKM-SNP.html

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

Freely downloadable

SOAP2
http://soap.genomics.org.cn/

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

Freely downloadable

FASTSNP
http://fastsnp.ibms.sinica.edu.tw/pages/input_CandidateGeneSearch.jsp

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

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

DOES NOT WORK

GenoA - Genome Analyzer
NOT AVAILABLE

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

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

Freely downloadable

SEAN
http://bioinformoodics.jhmi.edu/quickSNP.pl

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

Online

SNP500Cancer
http://genetics.bwh.harvard.edu/snp2rflp/

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

Online

SNPStats
http://bioinfo.iconcologia.net/snpstats/start.htm

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

Online

ALFRED
http://alfred.med.yale.edu/alfred/index.asp

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

Online

Panzea
http://www.panzea.org/

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

Online

Ecgene
http://genome.ewha.ac.kr/ECgene/

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

Online

IGG3
http://bioinfo.hku.hk:13080/iggweb/

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

Freely downloadable

LocusZoom
http://csg.sph.umich.edu/locuszoom/

1) To plot regional association results from genome-wide association scans or candidate gene studies. 2) Has chromosome postion & gene reference name & SNP reference name as input & is available free, online.

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

Online

LS-SNP
http://modbase.compbio.ucsf.edu/LS-SNP/

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

Online

Oryza SNP
http://www.oryzasnp.org/

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

Online

PANTHER Coding SNP Analysis Tool
http://www.pantherdb.org/tools/csnpScoreForm.jsp

Not available

Online

PEAS
not available

Not available

Quake
http://pupasview.ochoa.fib.es http://www.pupasnp.org.

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

1st webpage- not working & 2nd webpage in a different language.

SNPeffect v2.0
http://lpg.nci.nih.go

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

DOES NOT WORK

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

Freely downloadable

WHAP
http://pngu.mgh.harvard.edu/~purcell/whap/

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

Freely downloadable

F-SNP
http://compbio.cs.queensu.ca/F-SNP/

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.

2007

Online

HGVbase - Human Genome Variation Database
http://hgvbase.cgb.ki.se/

Fredman D, Siegfried M, Yuan YP, Bork P, Lehv�slaiho 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

Online

MODBASE
http://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi

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.

2008

Online

MutDB
http://mutdb.org/

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

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

DOES NOT WORK

SNP Resource for Rice Genetics and Breeding Based on Subspecies Indica and Japonica Genome Alignments
http://www.plantgenome.uga.edu/snp

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

DOES NOT WORK

SNPeffect
http://snpeffect.vib.be/

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

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

Online

ALOHOMORA
http://gmc.mdc-berlin.de/alohomora/

It facilitates genome-wide linkage studies performed with high-density single nucleotide polymorphism (SNP) marker panels such as 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

DOES NOT WORK

2SNP
http://alla.cs.gsu.edu/~software/2SNP/

1) Frequently case/control genotype data represents family trios consisting of two parents and one offspring. 2) This project explores disease susceptibility prediction on genotype/haplotype data. 3) PHASING METHOD BASED ON 2-SNP HAPLOTYPES. 4) 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

1) It considers both the read qualities as well as the reference genome's quality for detecting SNPs in the sequenced genome. Freely downloadable, Java 6

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/

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/

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.

2007

100

DOES NOT WORK

AutoSNPa
http://dna.leeds.ac.uk/autosnpa/

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.

Not available

100

Freely downloadable

BEAP
http://www.animalgenome.org/tools/beap/index.html

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/

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) It characterises 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. Input- rs ID species-human but regional population specific only. free, online & user freindly divides all SNPs & start SNP into various functional classes like coding,non coding,UTR's,3' & 5' regions,etc

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

Online

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.

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

DOES NOT WORK

CLUMP
http://www.smd.qmul.ac.uk/statgen/dcurtis/software.html

Not availablein PubMed

Not available

100

Freely downloadable

CLUMPHAP
http://www.smd.qmul.ac.uk/statgen/dcurtis/software.html

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
NOT AVAILABLE

Not available

100

Drug to SNP
http://ns.nihcgc.re.kr/ ljy75/Drug-SNP.html

Not available

100

DOES NOT WORK

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

DOES NOT WORK

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

DOES NOT WORK

FastEpistasis
http://www.vital-it.ch/software/FastEpistasis/

1)It computes tests of epistasis for a large number of SNP pairs. C,windows/linux & input=PLINK format

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

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

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

Not available

100

DOES NOT WORK

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 publically available databases i.e TSC,dbSNP,ALFRED,HGVbase & Celera genomics. 4.They have included 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

GCTA
http://gump.qimr.edu.au/gcta/

Estimate the proportion of phenotypic variance explained by genome/chromosome-wide SNPs for complex traits. 1) Estimate the genetic relationship from genome-wide SNPs. 2) Estimate the variance explained by all the autosomal SNPs. 3) Estimate the genetic variance associated with the X-chromosome. 4) Estimate the LD structure encompassing a list of target SNPs. species-human, C++, windows/linux/macOS freely downloadable.

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

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

DOES NOT WORK

GENECOUNTING
not available

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

genetic map position of SNPs
http://integrin.ucd.ie/cgi-bin/rs2cm.cgi

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

GENOTRACE
http://genotrace.niob.knaw.nl/

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/

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/welcome.do

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
not available

Not available

100

GEVALT - GEnotype Visualization and ALgorithmic Tool
http://acgt.cs.tau.ac.il/gevalt/

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

GLIDERS
http://mather.well.ox.ac.uk/GLIDERS/

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

GOLDsurfer
www.umbio.com along 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

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. input - SNP rs number,gene symbol,Haplotype: chromosome number, start position, end position.

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

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

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.

2007

100

Freely downloadable

HapBlock
http://www.cmb.usc.edu/msms/HapBlock/

1.To find 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

HaploBuild
http://snp.bumc.bu.edu/modules.php?name=HaploBuild

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

HaploSNPer
http://www.bioinformatics.nl/tools/haplosnper/

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/

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

DOES NOT WORK

HEPTAPLEX SNP
NOT AVAILABLE

Not available

100

InSNP
http://www.mucosa.de/insnp/

Manaster C, Zheng W, Teuber M, W�chter S, D�ring 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/

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

1) For detection of SNP in regulatory region i.e. whether it is affecting the transcription factor binding site or not. Input- text file with rs ID in line 1, 29 base pairs downstream of the SNP, Allele 1, 29 base pairs upstream of the SNP in line 2 & 29 b

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. input- SNPs with rs ids & chromosome position & snp chip data too.

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.

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

DOES NOT WORK

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

DOES NOT WORK

LDB2000
not available

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

LdCompare
http://www.affymetrix.com/support/developer/tools/devnettools.affx

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 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 rblocks, and haplotype frequencies. Example Output 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

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/

2009

100

Online

MapNext
not available

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

MAP-O-MAT
http://compgen.rutgers.edu/mapomat/

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, Hornsh�j H, Gorodkin J, Hedegaard J, Cirera S, Thomsen B, Madsen LB, H�j 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

DOES NOT WORK

MedRefSNP
http://www.medclue.com/ medrefsnp

Rhee H, Lee JS. MedRefSNP: a database of medically investigated SNPs. Hum Mutat. 2009 Mar;30(3):E460-6. PMID:19105187

2009

100

DOES NOT WORK

MicroSNiPer
http://cbdb.nimh.nih.gov/microsniper/

1) It examines the 3'-untranslated region and predicts if a SNP within the target site will disrupt or enhance a microRNA binding site. Species-human & online, free & nice user friendly.

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

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.Estimates 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 Estimates individual diplotypes and its respective frequencies. 3.Also estimates 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/

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, Standard Edition)

MQScore_SNP
http://mga.bionet.nsc.ru/soft/MQscore_SNP/

It does 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) input files- pedigree.csv -

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/

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

100

DOES NOT WORK

Mutation@A Glance
http://rapid.rcai.riken.jp/mutation/

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

novoSNP
http://www.molgen.ua.ac.be/bioinfo/novosnp/

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

In the pan-genome it finds SNPs in the core genome and determine the distribution of accessory genomic regions. Species-bacteria having pan genomes free,online.

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/

It checks the multiple comparisons at multiple SNP loci in linkage disequilibrium by treating linked loci as one haplotype block. Species-humans.

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

PARSESNP
http://www.proweb.org/parsesnp/

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/

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://149.166.112.99/peppi/

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

PGA - Power for Genetic Association analyses
http://pfs.nus.edu.sg/%28S%28xnqct0xfimmbnwwr2yw53lec%29%29/PFS_LogIn_V2.aspx

1) The putative function of the SNP as well as highlight if that a 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) Provide information of other previous reports that have examined the SNP-of-interest. 4) Provide information regarding the highest LD values (r2) of nearby pfSNPs. user friendly, free online, species-human inputs- 1) query to PFS database SNP:rsIDs, chromosome region.Gene: gene symbol,Tissue expression,GO term,KEGG pathway,mSigDB C2 pathway. GeneFunction/disease: Drug name, disease/genetic traits. 2) submit published SNP info

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

Online

PicSNP
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

Online registration

PolyDoms
http://mmb2.pcb.ub.es:8080/PMut/

Ferrer-Costa C, Gelp� 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

100

Online

PolyScan
http://genetics.bwh.harvard.edu/pph/

Predicts, if an amino acid substitution eventually affects a protein function, input-protein sequence & amino acid which is substituted by another & position of amino acid in protein sequence.

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

100

Online

POPTREE2
not available

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

Promolign
http://www.kms.ac.jp/~genomelb/takezaki/poptree2

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

Freely downloadable

PupasView
http://pupasuite.bioinfo.cipf.es/

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

100

Online registration

QuickSNP
http://www.cbcb.umd.edu/software/quake

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

100

Freely downloadable

Seq4SNPs
http://http//zebrafish.doc.ic.ac.uk/Sean

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.

2004

100

DOES NOT WORK

SeqDoC
http://www.srl.cam.ac.uk/oncology/bio/s4shome.html

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

Online

Seq-SNPing
not available

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

SimHap GUI
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

100

Online

SKM-SNP
not available

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

Snap - Single Nucleotide Polymorphism Annotation Platform
http://www-genepi.med.utah.edu/suppl/SLOPE/index.html

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

100

Program files available for download.

SNAP - Screening for non-acceptable polymorphisms
http://snap.humgen.au.dk/views/index.cgi

1) Input-gene name,chromosome location,marker position,clone & SNP rs ids. 2)Main-Detailed analysis of human genes and their variations. 3)A gene-gene relationship network on protein-protein interaction data, metabolic pathway connections and phylogenetic relations. 4)primer designing for amplification/seqeuncing of cDNA, genomic DNA, introns or exons. 5)SNPs affecting in RNA splicing. 6)Types of SNPs(synonymus,non-synonymus & in-dels), region where SNP is present in the gene/genome region. 7)Input-gene name-features obtained -Ensemble transcript Ids for all genes present in their database. -Clicking on one gene will give you all the above information mentioned. -input-tissue then it gives all genes expressed in that tissue which are present in their database & snps present in each of them. -input-disease-then all genes in that disease condition in their database is given.

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.

2006

100

Online

SNEP - Simultaneous detection of both nucleotide and expression polymorphisms
http://www.rostlab.org/services/SNAP

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

SNP Chart
http://www.elchtools.de/SNEP/

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 cherry picker
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

DOES NOT WORK

SNP Cutter
Author ID: SD@oxagen.co.uk

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

AVAILABALE FREE OF CHARGE ON REQUEST FROM AUTHORS

SNP ID-info
http://bioinfo.bsd.uchicago.edu/SNP_cutter.htm

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

Online

snp.plotter
http://bio.kuas.edu.tw/snpid-info

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

DOES NOT WORK

SNP@Domain
http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html

1. To produce images of genetic association results using single SNP and/or haplotype data with a corresponding LD heatmap in one correctly aligned graphic. 2. snp.plotter can plot 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@Ethnos
http://snpnavigator.net/

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

DOES NOT WORK

SNP@Evolution
http://variome.kobic.re.kr/SNPatETHNIC/

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@Promoter
http://bighapmap.big.ac.cn/

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_tools
NOT AVAILABLE

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

SNP2CAPS
not available

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

SNP2RFLP
http://pgrc.ipk-gatersleben.de/snp2caps/

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

Freely downloadable

SNPAnalyzer
http://variantgps.nci.nih.gov/cgfseq/pages/snp500.do

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

100

Online

SNPannotator
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

SNPator
http://dna.leeds.ac.uk/snpannotator/

Not available

100

Freely downloadable

SNPbox
http://www.snpator.org/public/new_login/index.php

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

SNPdetector
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. 6.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

SNPexp
http://snpeffect.vib.be/

2006

100

Online

SNP-Flankplus
http://app3.titan.uio.no/biotools/tool.php?app=snpexp

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

SNPforID browser
http://bio.kuas.edu.tw/snp-flankplus/

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

DOES NOT WORK

SNPHarvester
http://spsmart.cesga.es/help.php?dataSets[]=snpforid52

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

Online

SNPHunter
http://bioinformatics.ust.hk/SNPHarvester.html

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

Freely downloadable

SNPinfo
http://www.hsph.harvard.edu/ppg/software.htm

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

SNPit
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

Online

SNPLINK
not available

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

SNPmasker
http://webdocs.cs.ualberta.ca/~ghlin/src/WebTools/haplotyping.php

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

Freely downloadable

SNPNB
http://bioinfo.ebc.ee/snpmasker/

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

Online

SNP-o-matic
http://bioinfo.vipbg.vcu.edu/SNPNB/

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

DOES NOT WORK

SNPosition
http://snpomatic.sourceforge.net/

Manske HM, Kwiatkowski DP. SNP-o-matic. Bioinformatics. 2009 Sep 15;25(18):2434-5. Epub 2009 Jul 2. PubMed PMID: 19574284.

2009

100

Freely downloadable

SNPpy
NOT AVAILABLE

Not available

100

SNPrank
NOT AVAILABLE

Not available

100

SNPseek
http://www.snps3d.org/

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

100

Online

SNPselector
http://snp.wustl.edu/cgi-bin/SNPseek/index.cgi

Not available

100

Online

SNPServer
http://primer.duhs.duke.edu/

SNPselector: a web tool for selecting SNPs for genetic association studies. Xu H, Gregory SG, Hauser ER, Stenger JE, Pericak-Vance MA, Vance JM, Z�chner S, Hauser MA. Bioinformatics. 2005 Nov 15;21(22):4181-6. Epub 2005 Sep 22. PMID:16179360

2005

100

DOES NOT WORK

SNPsetter
http://hornbill.cspp.latrobe.edu.au/snpdiscovery.html.

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

DOES NOT WORK

SNPsFinder
http://dna.leeds.ac.uk/snpsetter/

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

SNPSplicer
http://gump.qimr.edu.au/general/daleN/SNPSpD/

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.

Not available

100

Online

SnpStation
http://www.ikmb.uni-kiel.de/snpsplicer/

ElSharawy A, Manaster C, Teuber M, Rosenstiel P, Kwiatkowski R, Huse K, Platzer M, Becker A, N�rnberg 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

Freely downloadable

MicroSNiPer
http://cbdb.nimh.nih.gov/microsniper

2010

100

Online

SNPtoGO
https://webtools.imbs.uni-luebeck.de/snptogo/

Schwarz DF, H�dicke O, Erdmann J, Ziegler A, Bayer D, M�ller S. SNPtoGO: characterizing SNPs by enriched GO terms. Bioinformatics. 2008 Jan 1;24(1):146-8. Epub 2007 Nov 17. PubMed PMID: 18024970.

2007

100

Freely downloadable

SNPTools
http://www.birc.au.dk/snptools

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

DOES NOT WORK

SNP-VISTA
http://genome.lbl.gov/vista/snpvista

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
not available

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

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/

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 displayed on website.

Not available

100

Freely downloadable

S2G - Syndrome to gene
http://fohs.bgu.ac.il/s2g/index.html

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

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/

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

The SNP ratio test
http://sourceforge.net/projects/snpratiotest/

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://www.ba.itb.cnr.it/BIG/UTRScan/

Not available

100

DOES NOT WORK

VarDetect
http://www4a.biotec.or.th/GI/tools/vardetect

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

Not available

100

Online

varLD
http://www.nus-cme.org.sg/software/varld.html

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
not available

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

WASP - Web-based Allele-Specific PCR
http://bioinfo.biotec.or.th/WASP

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

Not available

100

Online

A cSNP Map and Database for Human Chromosome 21
http://csnp.unige.ch/

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

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

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/

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.

2008

100

Online

BcSNPdb
http://snugenome.snu.ac.kr/BtcSNP/

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/

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/

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/

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

dbDNV
http://goods.ibms.sinica.edu.tw/DNVs/

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/polyreg/

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

DPDB - Drosophila polymorphism database
NOT AVAILABLE

Not available

100

FLYSNPdb
http://flysnp.imp.ac.at/flysnpdb.php

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

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

FunctSNP
NOT AVAILABLE

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

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/

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 and command line

Go!Poly
http://61.139.84.5/gopoly/

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

DOES NOT WORK

GoSh
http://www.itb.cnr.it/gosh/snps.php

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/resources/ web-resources/gwas-analyzer

1) It access to the data from a genome-wide association study of human susceptibility to bacterial infection. Species-human, free online, input-rs ID.

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
NOT AVAILABLE

Brookes AJ. HGBASE--a unified human SNP database. Trends Genet. 2001 Apr;17(4):229. PubMed PMID: 11357826.

2001

100

HLungDB
http://www.megabionet.org/bio/hlung

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

DOES NOT WORK

HSPVdb - Human Short Peptide Variation Database
http://srs.bioinformatics.nl/hspv/

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/

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

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.

Not available

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

Not available

100

Online

MamPol
http://mampol.uab.es/

Egea R, Casillas S, Fern�ndez 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

2006

100

Online

MamuSNP
http://mamusnp.ucdavis.edu/query.php

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/?sec=home

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/

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/ 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

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/

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://pda.uab.es/

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://149.166.112.99/peppi/

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

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/

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/

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

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

Rice genetic marker database
NOT AVAILABLE

Not available

100

rSNP_Guide
http://wwwmgs.bionet.nsc.ru/mgs/systems/rsnp/

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

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

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 dissection of phenotypic and genetic variation in Pacific white shrimp (Litopenaeus vannamei)
NOT AVAILABLE

2009

100

SNP Resource for Human Chromosome 22
NOT AVAILABLE

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

SNP-centric database
NOT AVAILABLE

Riva A, Kohane IS. A SNP-centric database for the investigation of the human genome. BMC Bioinformatics. 2004 Mar 26;5:33. Review. PubMed PMID: 15046636.

2004

100

SNPExpress
http://www.planetmathematics.com/SNPExpress/ OR http://people.chgv.lsrc.duke.edu/~dg48//SNPExpress/

Sanders MA, Verhaak RG, Geertsma-Kleinekoort WM, Abbas S, Horsman S, van der Spek PJ, L�wenberg 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 and command OR Online (2nd link) line

SNPnexus
http://www.snp-nexus.org/

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.

2008

100

Online

SNPSTR
http://www.sbg.bio.ic.ac.uk/~ino/cgi-bin/SNPSTRdatabase.html

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

SPSmart
http://spsmart.cesga.es/

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

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

DOES NOT WORK

T2D-Db
http://t2ddb.ibab.ac.in/home.shtml

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/

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

TcSNP
http://snps.tcruzi.org/

Ackermann AA, Carmona SJ, Ag�ero 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/

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

The catfish genome database cBARBEL (D-HaploDB)
http://orca.gen.kyushu-u.ac.jp/

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.

2006

100

Online

TOMATOMA
http://tomatoma.nbrp.jp/index.jsp

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/

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

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

Online

VarySysDB
http://h-invitational.jp/varygene/

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

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

DOES NOT WORK