ASmodeler: gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences
1 Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, Korea and 2 School of Chemistry, Seoul National University, Seoul 151-747, Korea
* To whom correspondence should be addressed. Tel: +82 232772888; Fax: +82 232772384; Email: sanghyuk{at}ewha.ac.kr
Received February 14, 2004; Revised March 9, 2004; Accepted March 29, 2004
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/.
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