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Bioinformatics Advance Access originally published online on July 22, 2004
Bioinformatics 2004 20(18):3697-3699; doi:10.1093/bioinformatics/bth431
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Bioinformatics vol. 20 issue 18 © Oxford University Press 2004; all rights reserved.

Applications Note

PCOAT: positional correlation analysis using multiple methods

Yuan Qi 2 and Nick V. Grishin 1,2,*

1 Howard Hughes Medical Institute and 2 Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050, USA

Received on June 10, 2004; revised on July 13, 2004; accepted on July 14, 2004
Advance Access Publication July 22, 2004

Summary: PCOAT (Positional COrrelation Analysis Tool) is a program to perform positional correlation analysis for protein multiple sequence alignment in order to identify structurally or functionally important interactions between positions in a protein family. We implement different statistical methods to detect highly correlated position pairs, amino acid pairs, individual positions and networks of correlated positions, and utilize multiple sequence weighting and sampling methods to eliminate background correlations caused by phylogeny and stochastic events. Our program runs relatively fast and is suitable for analyzing alignments containing large number of sequences.

Availability: ftp://iole.swmed.edu/pub/PCOAT/

Supplementary information: The PCOAT ftp site contains a detailed description of the program, and the results of PCOAT analysis on C2H2 alignment and ACT domain alignment.

Contact: grishin{at}chop.swmed.edu

* To whom correspondence should be addressed.


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