ASmodeler: Gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences

Namshin Kim, Seokmin Shin, Sanghyuk Lee

Research output: Contribution to journalArticlepeer-review

18 Scopus citations

Abstract

Alternative splicing is in important mechanism of modulating gene function and expression which greatly expands transcriptome diversity. ASmodeler is a novel web-based utility that finds gene models including alternative splicing events from genomic alignment of mRNA, EST and protein sequences. User-supplied sequences are aligned against the genome map using the BLAT and SIM4 programs. Resulting exon connectivity is analyzed by applying graph-theoretic methods to build all possible gene models including splice variants. The algorithm essentially combines the genome-based sequence clustering and transcript assembly procedures in a coherent fashion. In addition to the user-supplied sequences, UniGene clusters and many well-known gene predictions such as Genscan, Ensembl and Acembly may be included in gene modeling. The current implementation supports human, mouse and rat genomes. ASmodeler is available at http://genome.ewha.ac.kr/ECgene/ASmodeler/.

Original languageEnglish
Pages (from-to)W181-W186
JournalNucleic Acids Research
Volume32
Issue numberWEB SERVER ISS.
DOIs
StatePublished - 1 Jul 2004

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