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Bioinformatics Advance Access published online on February 26, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth150
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received December 19, 2003
Revised February 10, 2004
Accepted February 16, 2004

Applications note

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

Chesley M. Leslin 1, Alex Abyzov 1, Valentin A. Ilyin 1*

1 Department of Biology, Northeastern University, 360 Huntington Ave., Boston MA 02115, USA

* To whom correspondence should be addressed. E-mail: ilyin{at}neu.edu.


  Abstract

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 SEDB, Structural Exon Database, with a web interface, an application which allows users to retrieve the exon/intron organization of genes and map the location of the exon boundaries and 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


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