Nucleic Acids Research Advance Access published online on November 15, 2006
Nucleic Acids Research, doi:10.1093/nar/gkl884
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The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species
Department of Chemistry and Biochemistry, Center for Computational Biology Institute for Genomics and Proteomics, Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA 90095-1570, USA 1 Department of Biomathematics, David Geffen School of Medicine University of California Los Angeles, Los Angeles, CA 90095, USA
*To whom correspondence should be addressed. Tel: +1 310 825 7374; Fax: +1 310 206 7286; Email: leec{at}mbi.ucla.edu
Received September 15, 2006. Revised October 10, 2006. Accepted October 11, 2006.
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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