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Bioinformatics Advance Access published online on January 24, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl019
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received December 9, 2005
Revised January 18, 2006
Accepted January 23, 2006

Applications note

VISSA: a program to visualize structural features from structure sequence alignment

Weizhong Li 1 * and Adam Godzik 1

1 Burnham Institute for Medical Research, La Jolla, CA 92037, USA

* To whom correspondence should be addressed.
Weizhong Li, E-mail: liwz{at}burnham.org


  Abstract

Motivation: Multiple sequence alignment is an important tool to understand and analyze functions of homologous proteins. However, the logic of residue conservation/variation is usually apparent only in 3D space, not on a primary sequence level. Thus, in a traditional multiple alignment it is often difficult to directly visualize and analyze key residues because they are masked by other residues along the alignment. Here we present an integrated multiple alignment and 3D structure visualization program that can 1) map and highlight residues from a 1D alignment onto a 3D structure and vice versa, and 2) display only the alignment of preselected, key residues. This program, called VISSA (VIsualize Structure Sequence Alignment), also has many other built-in tools that can help analyze multiple sequence alignments.

Availability: http://bioinformatics.burnham.org/liwz/vissa.

Associate Editor: Dmitrij Frishman
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