title: 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 included in gene modeling. The current implementation supports human, mouse and rat genomes. ASmodeler is available at http://genome.ewha.ac.kr/ECgene/ASmodeler/.
authors.affiliation: Division of Molecular Life Sciences, Ewha Womans University, Seoul 120-750, Korea.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.forename: Seokmin
authors.initials: S
authors.lastname: Shin
authors.forename: Sanghyuk
authors.initials: S
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D000818:Animals; D005091:Exons; D020224:Expressed Sequence Tags / Q000737:chemistry; D016678:Genome; D006801:Humans; D020407:Internet; D051379:Mice; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012333:RNA, Messenger / Q000737:chemistry; D051381:Rats; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D017423:Sequence Analysis, RNA; D012984:Software; D014584:User-Computer Interface
chemical_list: D012333:RNA, Messenger