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Bioinformatics Advance Access originally published online on January 29, 2004
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Bioinformatics 20(6) © Oxford University Press 2004; all rights reserved.

Visualization of near-optimal sequence alignments

Michael E. Smoot 1, Stephanie A. Guerlain 1 and William R. Pearson 2,*

1 Department of Systems and Information Engineering and 2 Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA

Received on July 23, 2003 ; accepted on July 31, 2003
Advance Access Publication January 29, 2004

Motivation: Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful alignment in the potentially large set of options.

Results: We have developed Web-based software that displays near optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A WWW interface to a C++ program generates near optimal alignments, which are sent to a Java Applet, which displays them in a series of alignment frames. The Applet aligns residues so that consistently aligned regions remain at a fixed position on the display, while variable regions move. The display can be stopped to examine alignment details.

Availability: Available at http://fasta.bioch.virginia.edu/noptalign. For source code contact the authors at wrp{at}virginia.edu

Contact: wrp{at}virginia.edu

* To whom correspondence should be addressed.


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