Skip Navigation

Nucleic Acids Research 2005 33(Web Server Issue):W188-W192; doi:10.1093/nar/gki384
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2002K) Freely available
Right arrow Screen PDF (224K) Freely available
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 Garrow, A. G.
Right arrow Articles by Westhead, D. R.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Garrow, A. G.
Right arrow Articles by Westhead, D. R.
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
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}oupjournals.org

Article

TMB-Hunt: a web server to screen sequence sets for transmembrane ß-barrel proteins

Andrew G. Garrow, Alison Agnew and David R. Westhead*

School of Biochemistry and Microbiology, University of Leeds Leeds LS2 9JT, UK

*To whom correspondence should be addressed. Tel: +44 113 2333116; Fax: +44 113 2333167; Email: westhead{at}bmb.leeds.ac.uk

Received February 14, 2005. Revised March 9, 2005. Accepted March 9, 2005.

TMB-Hunt is a program that uses a modified k-nearest neighbour (k-NN) algorithm to classify protein sequences as transmembrane ß-barrel (TMB) or non-TMB on the basis of whole sequence amino acid composition. By including differentially weighted amino acids, evolutionary information and by calibrating the scoring, a discrimination accuracy of 92.5% was achieved, as tested using a rigorous cross-validation procedure. The TMB-Hunt web server, available at www.bioinformatics.leeds.ac.uk/betaBarrel, allows screening of up to 10 000 sequences in a single query and provides results and key statistics in a simple colour coded format.


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
 Nucleic Acids ResHome page
S. Montgomerie, J. A. Cruz, S. Shrivastava, D. Arndt, M. Berjanskii, and D. S. Wishart
PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W202 - W209.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. S. Wishart, D. Arndt, M. Berjanskii, A. C. Guo, Y. Shi, S. Shrivastava, J. Zhou, Y. Zhou, and G. Lin
PPT-DB: the protein property prediction and testing database
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D222 - D229.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Sundaresh, A. Randall, B. Unal, J. M. Petersen, J. T. Belisle, M. Gill Hartley, M. Duffield, R. W. Titball, D. H. Davies, P. L. Felgner, et al.
From protein microarrays to diagnostic antigen discovery: a study of the pathogen Francisella tularensis
Bioinformatics, July 1, 2007; 23(13): i508 - i518.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
M. M. Gromiha, Y. Yabuki, S. Kundu, S. Suharnan, and M. Suwa
TMBETA-GENOME: database for annotated {beta}-barrel membrane proteins in genomic sequences
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D314 - D316.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K.-J. Park, M. M. Gromiha, P. Horton, and M. Suwa
Discrimination of outer membrane proteins using support vector machines
Bioinformatics, December 1, 2005; 21(23): 4223 - 4229.
[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.