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Bioinformatics Advance Access originally published online on January 24, 2006
Bioinformatics 2006 22(7):887-888; 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

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

Weizhong Li * and Adam Godzik

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

*To whom correspondence should be addressed.

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 three-dimensional (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 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

Contact: liwz{at}burnham.org

Received on December 9, 2005; revised on January 18, 2006; accepted on January 23, 2006

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