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