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ECgene: Genome annotation for alternative splicing

Title
ECgene: Genome annotation for alternative splicing
Authors
Kim P.Kim N.Lee Y.Kim B.Shin Y.Lee S.
Ewha Authors
이상혁
SCOPUS Author ID
이상혁scopus
Issue Date
2005
Journal Title
Nucleic Acids Research
ISSN
0305-1048JCR Link
Citation
Nucleic Acids Research vol. 33, no. DATABASE ISS., pp. D75 - D79
Indexed
SCI; SCIE; SCOPUS WOS scopus
Document Type
Article
Abstract
ECgene provides annotation for gene structure, function and expression, taking alternative splicing events into consideration. The gene-modeling algorithm combines the genome-based expressed sequence tag (EST) clustering and graph-theoretic transcript assembly procedures. The website provides several viewers and applications that have many unique features useful for the analysis of the transcript structure and gene expression. The summary viewer shows the gene summary and the essence of other annotation programs. The genome browser and the transcript viewer are available for comparing the gene structure of splice variants. Changes in the functional domains by alternative splicing can be seen at a glance in the transcript viewer. We also provide two unique ways of analyzing gene expression. The SAGE tags deduced from the assembled transcripts are used to delineate quantitative expression patterns from SAGE libraries available publically. Furthermore, the cDNA libraries of EST sequences in each cluster are used to infer qualitative expression patterns. It should be noted that the ECgene website provides annotation for the whole transcriptome, not just the alternatively spliced genes. Currently, ECgene supports the human, mouse and rat genomes. The ECgene suite of tools and programs is available at http://genome.ewha. ac.kr/ECgene/. © Oxford University Press 2005; all rights reserved.
DOI
10.1093/nar/gki118
Appears in Collections:
자연과학대학 > 생명과학전공 > Journal papers
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