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A compilation and categorization of alternative splicing resources : Gene Information
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
EuGene'Hom
http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl
It is a gene prediction software for eukaryotic organisms based on comparative analysis.
Foissac S, Bardou P, Moisan A, Cros MJ, Schiex T. EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences. Nucleic AcIDs Res. 2003 Jul 1;31(13):3742-5. PubMed PMID: 12824408; PubMed Central PMCID: PMC168992.
2003
20
1)Gene information comprises of the number, strand, phase and Frame information. 2) The graphical output shows a)6 possible coding phases (+1, +2, +3 for the direct strand, -1, -2, -3 for the reverse one) b) introns on the forward (IF) and reverse (IR) strands c) other non coding regions (IG for intergenic or UTR regions) 3) Start, stop, donor and acceptor sites are marked on the graph. 4) The program is more specifically tuned for angiosperms.
AgenDA - Alignment based Gene Detection Algorithm
http://bibiserv.techfak.uni-bielefeld.de/agenda/
Gene prediction tool performing searches for conserved splice sites and start/stop codons. It also identifies potential exons.
Taher L, Rinner O, Garg S, Sczyrba A, Brudno M, Batzoglou S, Morgenstern B. AGenDA:homology-based gene prediction. Bioinformatics. 2003 Aug 12;19(12):1575-7. PubMed PMID: 12912840.
2003
99
1) Results are obtained in e-mail 2) Gene information provides Gene number. 3) Provides information about the reading frame (0,1,2) 4) Gives information about the DNA strand, whether + or -
Alexa-Seq - Alternative Expression Analysis By RNA Sequencing
http://www.alexaplatform.org/alexa_seq/index.htm
Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, Tang MJ, Hou YC, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li HI, McDonald H, Teague K, Zhao Y, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJ, Tai IT, Marra MA. Alternative expression analysis by RNA sequencing. Nat Methods. 2010 Oct;7(10):843-7. Epub 2010 Sep 12. PubMed PMID: 20835245.
2010
100
1) ALEXA-Seq annotation databases for eight species, raw data, source code, etc. can be downloaded. 2) Gene information includes chromosome number, start, end, strand, size and type of gene.
ASAP II - Alternative Splicing Annotation Project
http://bioinfo.mbi.ucla.edu/ASAP2/
Kim N, Alekseyenko AV, Roy M, Lee C. The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic AcIDs Res. 2007 Jan;35(Database issue):D93-8. Epub 2006 Nov 15. PubMed PMID: 17108355; PubMed Central PMCID: PMC1669709.
2006
100
1) Gives Genomic expression. 2) Gives Genomic location, gene aliases etc. as gene information. 3) Orthologous genes identified by MULTIZ alignments are given. 4) Isoform sequences are given. 5) Type of exons- Alternative or Constitute are given along with genomic position and number of EST and mRNA observed. 6) Intron type- Alternative or Constitutive, 5 site, 3 site, whether canonical or not and splice type, all information is provided. 7) Alternative Splicing information is provided.
asg - Alternative Splicing Gallery
http://statgen.ncsu.edu/asg/
It integrates transcript information into splicing graphs in order to visualize gene structure and alternative splicing.
Leipzig J, Pevzner P, Heber S. The Alternative Splicing Gallery (ASG): brIDging the gap between genome and transcriptome. Nucleic AcIDs Res. 2004 Aug 3;32(13):3977-83. Print 2004. PubMed PMID: 15292448; PubMed Central PMCID:PMC506815.
2004
100
Gene information includes chromosome number, start and end position, strand information.
ASIP - Alternative Splicing in Plants
http://www.plantgdb.org/ASIP/tools/
Search against Arabidopsis and rice introns/exons/exon junctions.
Not available
Not available
100
Gene information includes start and end position, chromosome number.
ASMD - Alternative Splicing Mutation Database
http://mco321125.meduohio.edu/~jbechtel/asmd/1.1/
It is used to check for the mutation that has been caused and the effect that happened because of the mutation. It also gives the type of mutation and the accuracy levels for that mutation.
Bechtel JM, Rajesh P, Ilikchyan I, Deng Y, Mishra PK, Wang Q, Wu X, Afonin KA, Grose WE, Wang Y, Khuder S, Fedorov A. The Alternative Splicing Mutation Database: a hub for investigations of alternative splicing using mutational evIDence. BMC Res Notes. 2008;1:3. Epub 2008 Feb 26. PubMed PMID: 18611286; PubMed Central PMCID: PMC2518265.
2008
100
1) ASMD data can be downloaded. 2) Gene information includes Exon number, position of mutation, mutation detail and codon change. 3) Wild type and mutated sequence are given. 4) Effects of mutation along with the number of exons affected, is mentioned.
ASPic - Alternative Splicing Prediction
http://t.caspur.it/ASPIC/index.php
1) Detect the exon-intron structure of a gene. 2) Predicts constitutive and alternative splice sites.
Bonizzoni P, Rizzi R, Pesole G. ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences. BMC Bioinformatics. 2005 Oct 5;6:244. PubMed PMID:16207377; PubMed Central PMCID: PMC1276783.
2005
100
1) Requires registration. 2) Gene name Brca1 and mybl2 as well as uploaded sequence didn't receive any results when used in the option of 'RUN Aspic'. 3) Provides option of retrieving Unigene ID for input. 4) Results are obtained in E-mail. 5) Gives genomic and transcript sequences. 6) Gene structure view is provided, showing Refseq exon, Novel exon, Refseq Intron, Novel intron, Fuzzy Intron, Canonical splice site and Non-Canonical splice site. 7) Shows 3'UTR and 5'UTR, Poly A site 8) Splice site details include the intron number, chromosome number, length, donor/ acceptor score, branching site score 9) Intron table provides information about relative and absolute start as well as relative and absolute end of intron, number of EST's, chromosome number, intron class, and Donor and acceptor site. 9) Gene information includes chromosome number, strand, position and length of gene.
ASTRA - Alternative Splicing and TRanscription Archives
http://alterna.cbrc.jp/
Database for identification of patterns of alternative splicing and transcriptional initiation. Exons introns structures of splice variants can be viewed on java applet.
Not available
Not available
100
1) Gene information includes Gene name, chromosome number, strand, position and number of patterns. 2) Sequence of gene can be downloaded. 3) Data of Alternative Splicing can also be downloaded.
fast DB - Friendly Alternative Splicing and Transcription Database
http://www.fast-db.com/
Easily and accurately defines the exon content of all known transcripts, produced by human genes.
de la Grange P, Dutertre M, Martin N, Auboeuf D. FAST DB: a website resource for the study of the expression regulation of human gene products. Nucleic AcIDs Res. 2005 Jul 28;33(13):4276-84. Print 2005. PubMed PMID: 16052034; PubMed Central PMCID: PMC1181862.
2005
100
Gene information includes description about the Gene, chromosome number, strand information.
GatExplorer - Genomic and Transcriptomic Explorer
http://bioinfow.dep.usal.es/xgate/principal.php
GATExplorer is an integrated database that combines genomic/transcriptomic visualization with nucleotide-level probe mapping.
Risueño A, Fontanillo C, Dinger ME, De Las Rivas J. GATExplorer: genomic and transcriptomic explorer; mapping expression probes to gene loci, transcripts, exons and ncRNAs. BMC Bioinformatics. 2010 Apr 29;11:221. PubMed PMID: 20429936; PubMed Central PMCID: PMC2875241.
2010
100
Gene information includes chromosome location and gene description.
GeneMark
http://exon.biology.gatech.edu/eukhmm.cgi#prot
Borodovsky M, Lomsadze A, Ivanov N, Mills R. Eukaryotic gene prediction using GeneMark.hmm. Curr Protoc Bioinformatics. 2003 May;Chapter 4:Unit4.6. PubMed PMID: 18428701.
2003
100
1) Results can be obtained by e-mail. 2) Gene information includes the Gene number and strand type. 3) Frame information is also given.
GOOD - Gene Oriented Ortholog Databse
http://goods.ibms.sinica.edu.tw/goods/index.html
Ho MR, Chen CH, Lin WC. Gene-oriented ortholog database: a functional comparison platform for orthologous loci. Database (Oxford). 2010;2010:baq002. Epub 2010 Feb 10. PubMed PMID: 20428317; PubMed Central PMCID: PMC2860896.
2010
100
1) Gives chromosome number and strand information as gene information. 2) Only the number of transcripts are given,which are linked to homologene (ncbi). 3) Also annotations from gene ontology are mentioned (molecular function, biological process, cellular component). 4) Reference transcripts, processed transcription units, orthologous tables, gene ontology can be downloaded. 5) Gives the detail of the different transcripts pertaining to that gene.
H-DBAS - Human Transcriptome Database for Alternative Splicing
http://jbirc.jbic.or.jp/h-dbas/
Takeda J, Suzuki Y, Sakate R, Sato Y, Gojobori T, Imanishi T, Sugano S. H-DBAS: human-transcriptome database for alternative splicing: update 2010. Nucleic AcIDs Res. 2010 Jan;38(Database issue):D86-90. Epub 2009 Dec 7. PubMed PMID: 19969536; PubMed Central PMCID: PMC2808982.
2010
100
1) Gene information gives chromosome number, position and strand. 2) Results can be downloaded. 3) Splice site details are shown graphically. 4) Also shows SNP in the graph. 5) Gene expression information is given, giving tissue specific expression in Affymetrix gene chip and Agilent. 6) Also gives information about Transcript feature.
ProSAS
http://services.bio.ifi.lmu.de/ProSAS/
Birzele F, Küffner R, Meier F, Oefinger F, Potthast C, Zimmer R. ProSAS: a database for analyzing alternative splicing in the context of protein structures. Nucleic AcIDs Res. 2008 Jan;36(Database issue):D63-8. Epub 2007 Oct 11. PubMed PMID: 17933774; PubMed Central PMCID: PMC2238869.
2008
100
1) Gene information includes chromosome number and strand information. 2) Returning database error as on 28th july 2012
SpliceCenter
http://projects.insilico.us/SpliceCenter/SpliceOverview.jsp
1)Displays gene splice variants and probe target locations for expression microarray platforms.  2)Provides a summary of splice variant coverage of multiple genes for common microarray platforms.  3)Provides high-througput analysis of peptide sequences indicating the splice variants that do / do not include the peptide. 
Ryan MC, Zeeberg BR, Caplen NJ, Cleland JA, Kahn AB, Liu H, Weinstein JN. SpliceCenter: a suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptIDe-based studies. BMC Bioinformatics. 2008 Jul 18;9:313. PubMed PMID: 18638396; PubMed Central PMCID: PMC2491637.
2008
100
1) Gene information includes the chromosome number, strand, start, stop. 2) Peptide check displays the coding sequence for a peptide within splice variant of a gene. 3) Expression- check provides visualization of microarray expression data for a gene 4) Batch tools are also provided.
SpliceMiner
http://projects.insilico.us/SpliceMiner/intro.jsp
SpliceMiner is a tool for querying Evidence Viewer Database (EVDB). SpliceMiner supports high-throughput batch queries and provides results in an easily parsable format.
Kahn AB, Ryan MC, Liu H, Zeeberg BR, Jamison DC, Weinstein JN. SpliceMiner: a high-throughput database implementation of the NCBI EvIDence Viewer for microarray splice variant analysis. BMC Bioinformatics. 2007 Mar 5;8:75. PubMed PMID: 17338820; PubMed Central PMCID: PMC1839109.
2007
100
1) Gene information includes chromosome number, start and end position, strand information. 2) Probe information includes Probe position.
U12DB - U12 Intron Database
http://genome.crg.es/cgi-bin/u12db/u12db.cgi
Alioto TS. U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic AcIDs Res. 2007 Jan;35(Database issue):D110-5. Epub 2006 Nov 1. PubMed PMID: 17082203; PubMed Central PMCID: PMC1635337.
2007
100
1) Didn't return any results with certain gene names like brca1 or mybl2. 2) Links to UCSC genome Browser is also given. 3) Intronic information is also given, such as junctions and sequence. 4) The donor, acceptor and branch point score is given under splice site details. 5) Gene information gives the description about the gene and the chromosome number.
 
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