ASPic - Alternative Splicing Prediction | Tool name | ASPic - Alternative Splicing Prediction |
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| URL | http://t.caspur.it/ASPIC/index.php |
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| Important features | 1) Detect the exon-intron structure of a gene. 2) Predicts constitutive and alternative splice sites. |
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| Citations | 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. |
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| Year of publication | 2005 |
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| Rank by usage frequency | 100 |
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| Comments | 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. |
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| Function | Exon detail, Exon detail: start/end, Exon detail: sequence, Exon detail: length, Exon detail indirect information, Intron detail, Intron detail: start/end, Intron detail: length, Graphical display of transcripts, Number of splice events, Splice site details, Predicted protein sequences, Gene Information, CDS details, Number of transcripts, Species, Finds alternative splicing in human, Finds alternative splicing in rat, Finds alternative splicing in mouse, Finds alternative splicing in chicken, Finds alternative splicing in dog, Finds alternative splicing in cow, Finds alternative splicing in other species |
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| Category | |
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| Input file format | FASTA file, Gene name, Chromosomal range, Transcript sequences, Unigene ID |
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| Output file format | |
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| Limitation | |
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