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

Title
ASmodeler: Gene modeling of alternative splicing from genomic alignment of mRNA, EST and protein sequences
Authors
Lee S.Kim N.Shin S.
Ewha Authors
이상혁
SCOPUS Author ID
이상혁scopus
Issue Date
2004
Journal Title
Nucleic Acids Research
ISSN
0305-1048JCR Link
Citation
Nucleic Acids Research vol. 32, no. WEB SERVER ISS., pp. W181 - W186
Indexed
SCI; SCIE; SCOPUS WOS scopus
Document Type
Article
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/. © Oxford University Press 2004; all rights reserved.
DOI
10.1093/nar/gkh404
Appears in Collections:
자연과학대학 > 생명과학전공 > Journal papers
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