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A compilation and categorization of alternative splicing resources : Finds alternative splicing in chicken
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
CONTRAST - CONditionally TRAined Search for Transcripts
http://contra.stanford.edu/contrast/
Predicts protein-coding genes from a multiple genomic alignment. It is designed for de novo predictions. It can also incorporate information from EST alignments.
Gross SS, Do CB, Sirota M, Batzoglou S. CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol. 2007;8(12):R269. PubMed PMID: 18096039; PubMed Central PMCID: PMC2246271.
2007
1
Predicitions downloadable or can be browsed by using UCSC genome browser.
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 -
BLAT - BLAST like Alignment tool
http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PubMed PMID: 11932250; PubMed Central PMCID: PMC187518.
2002
99
1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour.
C-It
http://C-It.mpi-bn.mpg.de
Gellert P, Jenniches K, Braun T, UchIDa S. C-It: a knowledge database for tissue-enriched genes. Bioinformatics. 2010 Sep 15;26(18):2328-33. Epub 2010 Jul 13. PubMed PMID: 20628071.
2010
99
1) Search results downloadable. 2) Gives links to all the pubmed articles mentioning the queried 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.
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.
ASPicDB - Alterenative Splicing Prediction database
http://t.caspur.it/ASPicDB/
Castrignan˛ T, D'Antonio M, Anselmo A, Carrabino D, D'Onorio De Meo A, D'Erchia AM, Licciulli F, Mangiulli M, Mignone F, Pavesi G, Picardi E, Riva A, Rizzi R, Bonizzoni P, Pesole G. ASPicDB: a database resource for alternative splicing analysis. Bioinformatics. 2008 May 15;24(10):1300-4. Epub 2008 Apr 3. PubMed PMID: 18388144.
2008
100
Astalavista - Alternative splicing transcriptional landscape visualization tool
http://genome.crg.es/astalavista/
Identifies complex Alternative Splice events by comparing all given transcripts.
Foissac S, Sammeth M. ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic AcIDs Res. 2007 Jul;35(Web Server issue):W297-9. Epub 2007 May 7. PubMed PMID: 17485470; PubMed Central PMCID: PMC1933205.
2007
100
1) The results can be browsed on UCSC browser. 2)Results can be downloaded in GTF or ASTA format. 3) Splice site details include the chromosome number, and the position of Alternative Splice sites. 4) Intron- Exon structure is also shown. 5) Types of Alternative Splice Events include exon skipping, alt acceptor and intron retention.
ChickGCE - Chicken Germ Cell EST
http://chickGCE.snu.ac.kr
1) Provides functional annotations, identification, and transcripts based on GEO.2) Provides comparison between two types of tissues and germ- cell- specific alternative splice events in the chicken.
Kim H, Lim D, Han BK, Sung S, Jeon M, Moon S, Kang Y, Nam J, Han JY. ChickGCE: a novel germ cell EST database for studying the early developmental stage in chickens. Genomics. 2006 Aug;88(2):252-7. Epub 2006 May 22. PubMed PMID: 16714094
2006
100
URL not working as on 14 Dec 2012
GeneSeqer
http://deepc2.psi.iastate.edu/cgi-bin/gs.cgi
Identify potential exon/intron structure in pre-mRNA by splice site prediction and spliced alignment.
Brendel V, Xing L, Zhu W. Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus. Bioinformatics. 2004 May 1;20(7):1157-69. Epub 2004 Feb 5. PubMed PMID: 14764557.
2004
100
1) Looks for the EST matches. 2) E-mail notification. 3) Specialized GeneSeqer server at PlantGDB is used to align plant sequences.
GenomeThreader
http://www.plantgdb.org/cgi-bin/GenomeThreader/gth.cgi
The GenomeThreader server allows you to perform spliced alignment of protein or EST/cDNA sequences to genomic DNA.
Not available
Not available
100
PolyA_DB 2
http://polya.umdnj.edu/PolyA_DB2
It specializes in identification of Poly-A tail.
Lee JY, Yeh I, Park JY, Tian B. PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes. Nucleic AcIDs Res. 2007 Jan;35(Database issue):D165-8. PubMed PMID: 17202160; PubMed Central PMCID: PMC1899096.
2007
100
URL not working as on 14 Dec 2012
Softberry
http://linux1.softberry.com/berry.phtml
1) Pattern based human gene structure prediction (multiple genes, both chains). 2) Find splice sites in genomic DNA using weight matrices. 3) BESTORF program analyses EST/mRNA sequences to predict potential coding fragments. 4) FGENE-SH is human gene prediction that allows to predict genes containing minor variants of donor splice sites (GC sites). 5) Looks for Pattern-based human multiple variants (alternative splicing) of potential genes in genomic DNA. 6) Finding potential 5'-, internal and 3'-coding exons. 7) Rna SPL is used for For exon-exon junctions positions in human cDNA.
Not available
Not available
100
SplicePredictor
http://deepc2.psi.iastate.edu/cgi-bin/sp.cgi
Identifies potential splice sites in (plant) pre-mRNA.
Not available
Not available
100
1) Gives information about acceptor and donor site. 2) Gives information about site location and sequence. 3) Also gives information about the site quality. 4) Results can be obtained by e-mail.
 
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