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@virginia.edu

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Author notes

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