Skip Navigation



Bioinformatics Advance Access published online on July 22, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth431
Bioinformatics © Oxford University Press 2004; all rights reserved
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
20/18/3697    most recent
bth431v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Qi, Y.
Right arrow Articles by Grishin, N. V.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Qi, Y.
Right arrow Articles by Grishin, N. V.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received June 10, 2004
Revised July 13, 2004
Accepted July 14, 2004

Applications note

PCOAT: positional correlation analysis using multiple methods

Yuan Qi 1 Nick V. Grishin 2*

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

* To whom correspondence should be addressed. E-mail: grishin{at}chop.swmed.edu.


  Abstract

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.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.