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Bioinformatics Advance Access originally published online on July 29, 2004
Bioinformatics 2004 20(18):3702-3704; doi:10.1093/bioinformatics/bth444
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Applications Note

CLANS: a Java application for visualizing protein families based on pairwise similarity

Tancred Frickey and Andrei Lupas *

Max Planck Institut fuer Entwicklungsbiologie, Spemannstrasse 35, 72076 Tuebingen, Germany

Received on April 8, 2004; revised on July 9, 2004; accepted on July 26, 2004
Advance Access Publication July 29, 2004

Summary: The main source of hypotheses on the structure and function of new proteins is their homology to proteins with known properties. Homologous relationships are typically established through sequence similarity searches, multiple alignments and phylogenetic reconstruction. In cases where the number of potential relationships is large, for example in P-loop NTPases with many thousands of members, alignments and phylogenies become computationally demanding, accumulate errors and lose resolution. In search of a better way to analyze relationships in large sequence datasets we have developed a Java application, CLANS (CLuster ANalysis of Sequences), which uses a version of the Fruchterman–Reingold graph layout algorithm to visualize pairwise sequence similarities in either two-dimensional or three-dimensional space.

Availability: CLANS can be downloaded at http://protevo.eb.tuebingen.mpg.de/download

Contact: andrei.lupas{at}tuebingen.mpg.de

* To whom correspondence should be addressed.


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