Skip Navigation


Nucleic Acids Research Advance Access originally published online on June 21, 2007
Nucleic Acids Research 2007 35(Web Server issue):W495-W498; doi:10.1093/nar/gkm406
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (7637K) Freely available
Right arrow Screen PDF (759K) Freely available
Right arrow Supplementary Material
Right arrowOA All Versions of this Article:
35/suppl_2/W495    most recent
gkm406v1
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 arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Feenstra, K. A.
Right arrow Articles by Heringa, J.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Feenstra, K. A.
Right arrow Articles by Heringa, J.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2007, Vol. 35, No. suppl_2 W495-W498
© 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/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

Sequence harmony: detecting functional specificity from alignments

K. Anton Feenstra1, Walter Pirovano1, Klaas Krab2 and Jaap Heringa2,*

1Centre for Integrative Bioinformatics VU (IBIVU) and 2Institute of Molecular Cell Biology, Vrije Universiteit Amsterdam, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +31 20 598 7649; Fax: +31 20 598 7653; Email: heringa{at}few.vu.nl

Received January 31, 2007. Revised April 5, 2007. Accepted May 3, 2007.

Multiple sequence alignments are often used for the identification of key specificity-determining residues within protein families. We present a web server implementation of the Sequence Harmony (SH) method previously introduced. SH accurately detects subfamily specific positions from a multiple alignment by scoring compositional differences between subfamilies, without imposing conservation. The SH web server allows a quick selection of subtype specific sites from a multiple alignment given a subfamily grouping. In addition, it allows the predicted sites to be directly mapped onto a protein structure and displayed. We demonstrate the use of the SH server using the family of plant mitochondrial alternative oxidases (AOX). In addition, we illustrate the usefulness of combining sequence and structural information by showing that the predicted sites are clustered into a few distinct regions in an AOX homology model. The SH web server can be accessed at www.ibi.vu.nl/programs/seqharmwww.


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


This article has been cited by other articles:


Home page
 BioinformaticsHome page
K. Ye, K. Anton Feenstra, J. Heringa, A. P. IJzerman, and E. Marchiori
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting
Bioinformatics, January 1, 2008; 24(1): 18 - 25.
[Abstract] [Full Text] [PDF]


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.