147. ASDB: Database of Alternatively Spliced Genes 

M. S. Gelfand, I. Dubchak, I. Dralyuk, and M. Zorn 
Institute of Protein Research, Russian Academy of Sciences, Pushchino, 142292, Russia and National Energy Research Scientific Computing Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 
ildubchak@lbl.gov 

Alternative splicing is an important regulatory mechanism in higher eukaryotes¹. By recent estimates, at least 30% of human genes are spliced alternatively (Mironov, A.A. and Gelfand, M.S. Proc. 1st Int. Conf. on Bioinformatics of Genome Regulation, 1998. v. 2, p. 249). Alternative splicing plays a major role in sex determination in Drosophila, antibody response in humans and other tissue or developmental stage specific processes^2-5. The database of alternatively spliced genes can be of potential use for molecular biologists studying splicing, developmental biologists, geneticists, and cell biologists. Version 1.1 of ASDB contains information about protein products of alternatively spliced genes. Selecting all SwissProt entries containing the words "alternative splicing" has generated 1663 proteins. Then clusters of proteins that could arise by alternative splicing of the same gene were created. Two proteins from the same species belong to a cluster if they have common fragments not shorter than 20 amino acids. Each cluster is represented in the database by the multiple global alignment of its members, allowing for easy identification of regions produced by alternative splicing. The database contains 241 clusters with more than one member. The database can be searched using Medline, SwissProt, and GenBank identifiers and accession numbers. Standard context search can be performed over SwissProt keyword, description, taxonomy, and comment fields and feature tables. ASDB contains internal links between entries and/or clusters, as well as external links to Medline, GenBank and SwissProt entries. Next steps of ASDB development will be incorporation of DNA data, classification of main types of alternative splicing, incorporation of data on aberrant splicing and splicing mutations. Automated processing of existing databases with minimum manual curation produced the current version of the database. In future we plan to add manual curation of the database, including addition of splicing variants described in the literature but not annotated in GenBank. 

AVAILABILITY 

ASDB is currently available at the URL http://hazelton.lbl.gov/~teplitski/alt/. The administrator of the database can be contacted by Email: asdb@lbl.gov. 

REFERENCES 

¹Sharp, P.A. (1994) Cell. 77, 805-815 
²Stamm, S.; Zhang, M.Q.; Marr, T.G. and Helfman, D.M. (1994) Nucleic Acids Res. 22,1515-26. 
³Chabot, B. (1996) Trends Genet. 12, 472-478 
⁴ Breitbart, R.E., Andreadis, A. and Nadal-Ginard, B. (1987) Annu. Rev. Biochem. 56, 467-495 
⁵Smith, C.W., Patton, J.G., and Nadal-Ginard, B. (1989) Annu. Rev. Genet. 23, 527-577