9th Annual Workshop, October 28-31, 1999
Co-sponsored by the U.S. Department of Energy
ASDB: Novel database of alternatively spliced genes
I. Dubchak1, M. S. Gelfand2, I. Dralyuk1, M. Zorn1, S. Spengler1
1National Energy Research Scientific Computing Center, Lawrence
Berkeley National Laboratory, Berkeley, California, USA
2Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia
Alternative splicing is an important regulatory mechanism in higher eukaryotes. By recent estimates, at least 30% of human genes are spliced alternatively (1). Alternative splicing plays a major role in sex determination in Drosophila, antibody response in humans and other tissue or developmental stage specific processes. The database of alternatively spliced genes can be of potential use for molecular biologists studying splicing, developmental biologists, geneticists, and cell biologists. We have created a public Alternative Splicing Database (ASDB) (2) for the biological community as a repository of data on alternatively spliced genes. ASDB is currently available at the URL http://hazelton.lbl.gov/~teplitski/alt/. The administrator of the database can be contacted by Email: firstname.lastname@example.org.
Our original set of 1663 proteins was generated by selecting all SwissProt entries containing the words "alternative splicing". Clusters of proteins that could arise by alternative splicing of the same gene were created by a string comparison procedure. Two proteins from the same species were considered belonging 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.
The next step in ASDB development will involve building a nucleotide division of ASDB by incorporating DNA data from GenBank and other sources, classification of the main types of alternative splicing, and adding data on aberrant splicing and splicing mutations.
1. Mironov, A.A. and Gelfand, M.S. Proc. 1st Int. Conf. on Bioinformatics of
Genome Regulation, 1998. v. 2, p. 249.
2. Gelfand, M., Dubchak, I., Dralyuk, I., M.Zorn. Nucl.Acids.Res. 1999, 27, 301-302.