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

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 in

SUBMITTER: Kim N 

PROVIDER: S-EPMC441542 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature