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A compilation and categorization of alternative splicing resources : Finds alternative splicing in Drosophila
Resources Important features / utilities*CitationsYear of publicationRank by usage frequency Click to Edit / Add comments
CONTRAST - CONditionally TRAined Search for Transcripts
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.

Predicitions downloadable or can be browsed by using UCSC genome browser.
BDGP - Berkeley Drosophila Genome Project
Used to predict the splite sites with the help of neural networks. It shows the intron/exon boundary as well.
Spradling AC, Stern D, Beaton A, Rhem EJ, Laverty T, Mozden N, Misra S, Rubin GM. The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes. Genetics. 1999 Sep;153(1):135-77. PubMed PMID: 10471706; PubMed Central PMCID: PMC1460730.

1) Splice Site details include start position, end position and score for acceptor as well as donor sites. 2) The exon/Intron boundary is shown by enlarging the font size.
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; PubMed Central PMCID: PMC1716719.

URL working but not leading to any result page after the query has been given.
Stanke M, Keller O, Gunduz I, Hayes A, Waack S, Morgenstern B. AUGUSTUS: ab initio prediction of alternative transcripts. Nucleic AcIDs Res. 2006 Jul 1;34(Web Server issue):W435-9. PubMed PMID: 16845043; PubMed Central PMCID: PMC1538822.

1) This method allows approximation of the true intron length distribution more accurately than do existing programs. 2) It gives alignment results.These can be downloaded as well. 3) Gives predicted coding sequences.
BLAT - BLAST like Alignment tool
Kent WJ. BLAT--the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PubMed PMID: 11932250; PubMed Central PMCID: PMC187518.

1) Link to UCSC Genome browser is given. 2) Splice Sites are marked in the sequence itself, with light blue colour.
Munch K, Krogh A. Automatic generation of gene finders for eukaryotic species. BMC Bioinformatics. 2006 May 21;7:263. PubMed PMID: 16712739; PubMed Central PMCID: PMC1522026.

"1) Requires registration. 2) Returns error ""Please note that this software is no longer being supported or updated."" as on 26th july 2012 3) GeneMachine is available by anonymous FTP at ftp://ftp.nhgri.nih.gov/pub/software/genemachine/."
AS-ALPS - Alternative Splicing Induced Alteration of Protein Structure
Shionyu M, Yamaguchi A, Shinoda K, Takahashi K, Go M. AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. Nucleic AcIDs Res. 2009 Jan;37(Database issue):D305-9. Epub 2008 Nov 10. PubMed PMID: 19015123; PubMed Central PMCID: PMC2686549.

1) Alternative Splicing type and position is given. 2) Uninformative transcripts can also be seen. 3) Splice site details include the position of the Alternative spliced region.
ASRG - ArabidopsisSplicing Related Genes
Wang BB, Brendel V. The ASRG database: identification and survey of Arabidopsis thaliana genes involved in pre-mRNA splicing. Genome Biol. 2004;5(12):R102. Epub 2004 Nov 29. PubMed PMID: 15575968; PubMed Central PMCID:PMC545797.

1) Didn't return any results using search fields when tried multiple times. 2) Browsing results not displayed properly due to some error in page.
Astalavista - Alternative splicing transcriptional landscape visualization tool
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.

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.
ASTRA - Alternative Splicing and TRanscription Archives
Database for identification of patterns of alternative splicing and transcriptional initiation. Exons introns structures of splice variants can be viewed on java applet.
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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.
BGF - Beijing Gene Finder
BGF is a gene finding program based on DP(Dynamic Programming) & HSMM(HIDden Semi-Markov Model).
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DEDB - Drosophila melanogaster Exon Database
It includes information on the exons of Drosophila melanogaster in a splicing graph form. A splicing graph viewer is available to visualize the splicing graph, which allows to check for the various forms of alternative splicing variants in an easy to understand way.
Lee BT, Tan TW, Ranganathan S. DEDB: a database of Drosophila melanogaster exons in splicing graph form. BMC Bioinformatics. 2004 Dec 7;5:189. PubMed PMID: 15581431; PubMed Central PMCID: PMC538278.
1) Predicts TATA box(i.e, TATA box pattern and position) and Poly-A site prediction(i.e, position and pattern). 2) Gives view of transcription factors.
Milanesi L, D'Angelo D, Rogozin IB. GeneBuilder: interactive in silico prediction of gene structure. Bioinformatics. 1999 Jul-Aug;15(7-8):612-21. PubMed PMID: 10487869.

Gene model and Coding potential are shown graphically, but are not loading as on 25th july 2012
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.

1) Results can be obtained by e-mail. 2) Gene information includes the Gene number and strand type. 3) Frame information is also given.
GeneNest is a comprehensive visualization of gene indices of the organisms. The aim of GeneNest is to represent each gene by a single cluster of ESTs and/or mRNAs.
Haas SA, Beissbarth T, Rivals E, Krause A, Vingron M. GeneNest: automated generation and visualization of gene indices. Trends Genet. 2000 Nov;16(11):521-3. PubMed PMID: 12199289.
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.

1) Looks for the EST matches. 2) E-mail notification. 3) Specialized GeneSeqer server at PlantGDB is used to align plant sequences.
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"1) Results can be obtained by E-mail. 2) Returns an error ""Use of uninitialized value in string eq at /export/www/cgi-bin/cbcb/genesplicer/gspl_cgi.cgi line 162, line 162."" after multiple tries"
Genie - Gene Finder Based on Generalized HIDden Markov Models
Reese MG, Eeckman FH, Kulp D, Haussler D. Improved splice site detection in Genie. J Comput Biol. 1997 Fall;4(3):311-23. PubMed PMID: 9278062.

No search option provided.
The GenomeThreader server allows you to perform spliced alignment of protein or EST/cDNA sequences to genomic DNA.
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GenView 2
Ronneberg TA, Freeland SJ, Landweber LF. Genview and Gencode : a pair of programs to test theories of genetic code evolution. Bioinformatics. 2001 Mar;17(3):280-1. PubMed PMID: 11294793.

1) Results can be mailed to the user as per his/her choice. 2) The result page is not returning any results except the sequence and the translated peptide sequence that has been submitted as on25-july-2012
SEE ESE - Sequence Evaluator for ESE
Identifies Exon splicing enhancers.
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1) Results can be obtained by E-mail. 2) Gives position, Motif and score as a result. 3) Graphic output can also be seen.
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.
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Aligns spliced sequences to genomic sequences, using local alignment algorithms and heuristics to put together a global spliced alignment. Spidey can produce reliable alignments quickly, even when confronted with noise from alternative splicing, polymorphisms, sequencing errors, or evolutionary divergence.
Wheelan SJ, Church DM, Ostell JM. SpIDey: a tool for mRNA-to-genomic alignments. Genome Res. 2001 Nov;11(11):1952-7. PubMed PMID: 11691860; PubMed Central PMCID: PMC311166.
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.

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 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.

1) Gene information includes chromosome number, start and end position, strand information. 2) Probe information includes Probe position.
Identifies potential splice sites in (plant) pre-mRNA.
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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.
Predicts splice signals.
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The position of acceptor and donor site is given along with intronic and exonic sequence as well as score.
U12DB - U12 Intron Database
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.

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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