Skip Navigation


Bioinformatics Advance Access originally published online on August 16, 2005
Bioinformatics 2005 21(20):3824-3831; doi:10.1093/bioinformatics/bti627
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary Data
Right arrow A correction has been published
Right arrowOA All Versions of this Article:
21/20/3824    most recent
bti627v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
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 ISI Web of Science
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 Search for citing articles in:
ISI Web of Science (3)
Google Scholar
Right arrow Articles by Price, G. A.
Right arrow Articles by Brenner, S. E.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Price, G. A.
Right arrow Articles by Brenner, S. E.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap

Gavin A. Price 1, Gavin E. Crooks 2, Richard E. Green 2 and Steven E. Brenner 1,2,*

1Department of Bioengineering, University of California Berkeley, CA 94720, USA
2Department of Plant and Microbial Biology, University of California Berkeley, CA 94720, USA

*To whom correspondence should be addressed at Department of Plant and Microbial Biology, 111 Koshland Hall #3102, University of California, Berkeley, CA 94720-3102, USA

Motivation: Protein sequence comparison methods are routinely used to infer the intricate network of evolutionary relationships found within the rapidly growing library of protein sequences, and thereby to predict the structure and function of uncharacterized proteins. In the present study, we detail an improved statistical benchmark of pairwise protein sequence comparison algorithms. We use bootstrap resampling techniques to determine standard statistical errors and to estimate the confidence of our conclusions. We show that the underlying structure within benchmark databases causes Efron's standard, non-parametric bootstrap to be biased. Consequently, the standard bootstrap underpredicts average performance when used in the context of evaluating sequence comparison methods. We have developed, as an alternative, an unbiased statistical evaluation based on the Bayesian bootstrap, a resampling method operationally similar to the standard bootstrap.

Results: We apply our analysis to the comparative study of amino acid substitution matrix families and find that using modern matrices results in a small, but statistically significant improvement in remote homology detection compared with the classic PAM and BLOSUM matrices.

Availability: The sequence sets and code for performing these analyses are available from http://compbio.berkeley.edu/.

Contact: brenner{at}compbio.berkeley.edu

Received on April 14, 2005; revised on July 16, 2005; accepted on August 11, 2005

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
E. L. Peterson, J. Kondev, J. A. Theriot, and R. Phillips
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment
Bioinformatics, June 1, 2009; 25(11): 1356 - 1362.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Wong and M. A. Ragan
MACHOS: Markov clusters of homologous subsequences
Bioinformatics, July 1, 2008; 24(13): i77 - i85.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. Stojmirovic, E. M. Gertz, S. F. Altschul, and Y.-K. Yu
The effectiveness of position- and composition-specific gap costs for protein similarity searches
Bioinformatics, July 1, 2008; 24(13): i15 - i23.
[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.