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ASAP II


NAR Molecular Biology Database Collection entry number 414
Kim N.1, Alekseyenko A.2, Roy M.1 and Lee C.1
1Department of Chemistry and Biochemistry, Center for Computational Biology, Institute for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1570, USA
2Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA

Database Description

We have greatly expanded the Alternative Splicing Annotation Project (ASAP, http://www.bioinformatics.ucla.edu/ASAP) database:
i) its human alternative splicing data is expanded about 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 ~ 3 fold expansion in detection of tissue-specific alternative splicing events, and of cancer vs. 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.

Recent Developments

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 and etc. ASAP II is available at http://www.bioinformatics.ucla.edu/ASAP2.

Acknowledgements

We wish to thank Calvin Pan, Qi Wang and Dr. Yi Xing for valuable comments on this work. This work has been supported by NIH grant U54 RR021813, Department of Energy grant DE-FC02-02ER63421, and by a Dreyfus Foundation Teacher-Scholar Award to C.J.L.

References


1. Lee, C., Atanelov, L., Modrek, B. and Xing, Y. (2003) ASAP: the Alternative Splicing Annotation Project. Nucleic Acids Res, 31, 101-105.
2. Modrek, B., Resch, A., Grasso, C. and Lee, C. (2001) Genome-wide detection of alternative splicing in expressed sequences of human genes. Nucleic Acids Res, 29, 2850-2859.
3. Kim, P., Kim, N., Lee, Y., Kim, B., Shin, Y. and Lee, S. (2005) ECgene: genome annotation for alternative splicing. Nucleic Acids Res, 33, D75-79.
4. Kim, N., Shin, S. and Lee, S. (2005) ECgene: genome-based EST clustering and gene modeling for alternative splicing. Genome Res, 15, 566-576.
5. Xu, Q. and Lee, C. (2003) Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences. Nucleic Acids Res, 31, 5635-5643.
6. Xu, Q., Modrek, B. and Lee, C. (2002) Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res, 30, 3754-3766.
7. Resch, A., Xing, Y., Alekseyenko, A., Modrek, B. and Lee, C. (2004) Evidence for a subpopulation of conserved alternative splicing events under selection pressure for protein reading frame preservation. Nucleic Acids Res, 32, 1261-1269.
8. Roy, M., Xu, Q. and Lee, C. (2005) Evidence that public database records for many cancer-associated genes reflect a splice form found in tumors and lack normal splice forms. Nucleic Acids Res, 33, 5026-5033.
9. Chen, F.C., Wang, S.S., Chen, C.J., Li, W.H. and Chuang, T.J. (2006) Alternatively and constitutively spliced exons are subject to different evolutionary forces. Mol Biol Evol, 23, 675-682.
10. Xing, Y., Wang, Q. and Lee, C. (2006) Evolutionary divergence of exon flanks: a dissection of mutability and selection. Genetics, 173, 1787-1791.


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