title: The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species.
abstract: We have greatly expanded the Alternative Splicing Annotation Project (ASAP) database: (i) its human alternative splicing data are expanded approximately 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 approximately 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.
authors.affiliation: 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.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.forename: Alexander V
authors.initials: AV
authors.lastname: Alekseyenko
authors.forename: Meenakshi
authors.initials: M
authors.lastname: Roy
authors.forename: Christopher
authors.initials: C
authors.lastname: Lee
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D030561:Databases, Nucleic Acid; D005091:Exons; D023281:Genomics; D006801:Humans; D020407:Internet; D007438:Introns; D022821:RNA Splice Sites; D016415:Sequence Alignment; D014584:User-Computer Interface
chemical_list: D022821:RNA Splice Sites