The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species

Kim, N.; Alekseyenko, A. V.; Roy, M.; Lee, C.

doi:10.1093/nar/gkl884

Title: The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species

Journal Article · Wed Nov 15 00:00:00 EST 2006 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkl884· OSTI ID:1625411

Kim, N. ^[1]; Alekseyenko, A. V. ^[2]; Roy, M. ^[1]; Lee, C. ^[1]

Univ. of California, Los Angeles, CA (United States). Inst. for Genomics and Proteomics. Molecular Biology Inst. Center for Computational Biology. Dept. of Chemistry and Biochemistry
Univ. of California, Los Angeles, CA (United States). David Geffen School of Medicine. Dept. of Biomathematics

We have greatly expanded the Alternative Splicing Annotation Project (ASAP) database: (i) its human alternative splicing data are expanded ~3-fold over the previous ASAP database, to nearly 90 000 distinct alternative splicing events; (ii) it now provides genome-wide alternative splicing analyses for 15 vertebrate, insect and other animal species; (iii) it provides comprehensive comparative genomics information for comparing alternative splicing and splice site conservation across 17 aligned genomes, based on UCSC multigenome alignments; (iv) it provides an 2- to 3-fold expansion in detection of tissue-specific alternative splicing events, and of cancer versus normal specific alternative splicing events. We have also constructed a novel database linking orthologous exons and orthologous introns between genomes, based on multigenome alignment of 17 animal species. It can be a valuable resource for studies of gene structure evolution. ASAP II provides a new web interface enabling more detailed exploration of the data, and integrating comparative genomics information with alternative splicing data. We provide a set of tools for advanced data-mining of ASAP II with Pygr (the Python Graph Database Framework for Bioinformatics) including powerful features such as graph query, multigenome alignment query, etc. ASAP II is available at http://www. bioinformatics.ucla.edu/ASAP2.

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Research Organization:: Univ. of California, Los Angeles, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; National Institutes of Health (NIH)

Grant/Contract Number:: FC02-02ER63421; U54 RR021813

OSTI ID:: 1625411

Journal Information:: Nucleic Acids Research, Vol. 35, Issue Database; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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