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Bioinformatics Advance Access originally published online on May 12, 2007
Bioinformatics 2007 23(14):1837-1839; doi:10.1093/bioinformatics/btm256
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/rcial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Rapid assessment of correlated amino acids from pair-to-pair (P2P) substitution matrices

Eran Eyal 1,*, Shmuel Pietrokovski 2 and Ivet Bahar 1

1Department of Computational Biology, School of Medicine, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, PA 15213, USA and 2Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel

*To whom correspondence should be addressed.


  Abstract

Identification of correlated amino acids in proteins has been a topic of broad interest in view of its functional implications and importance in protein design. A new set of pair-to-pair (P2P) substitution matrices for amino acids was recently introduced as a useful tool for inferring information on such correlated sites. We present a website developed for automated application of these matrices for analysis of query sequences. The site offers options for graphical analysis of correlations, as well as visualization of correlated amino acids on representative, structurally characterized, members of the examined family of sequences.

Availability: http://www.ccbb.pitt.edu/p2p

Contact: eyal{at}ccbb.pitt.edu

Associate Editor: Burkhard Rost

Received on February 2, 2007; revised on April 18, 2007; accepted on May 7, 2007

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