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Bioinformatics Advance Access originally published online on February 26, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.

Applications Note

Structural exon database, SEDB, mapping exon boundaries on multiple protein structures

Chesley M. Leslin , Alex Abyzov and Valentin A. Ilyin *

Department of Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA

Received on December 19, 2003; revised on February 10, 2003; accepted on February 16, 2004
Advance Access Publication February 26, 2004

Summary: Comparative analysis of exon/intron organization of genes and their resulting protein structures is important for understanding evolutionary relationships between species, rules of protein organization and protein functionality. We present Structural Exon Database (SEDB), with a Web interface, an application that allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and the intron phase onto a multiple structural alignment. SEDB is linked with Friend, an integrated analytical multiple sequence/structure viewer, which allows simultaneous visualization of exon boundaries on structure and sequence alignments. With SEDB researchers can study the correlations of gene structure with the properties of the encoded three-dimensional protein structures across eukaryotic organisms.

Availability: SEDB is publicly available at http://glinka.bio.neu.edu/SEDB/SEDB.html

Supplementary information: On the SEDB Web site.

Contact: ilyin{at}neu.edu

* To whom correspondence should be addressed.


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