Skip Navigation



Bioinformatics Advance Access published online on September 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti035
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:
21/4/542    most recent
bti035v1
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 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 Kisman, D.
Right arrow Articles by Wang, L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kisman, D.
Right arrow Articles by Wang, L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Received July 14, 2004
Revised September 3, 2004
Accepted September 10, 2004

Applications note

TPatternHunter: Gapped, fast and sensitive translated homology search

Derek Kisman 1, Ming Li 2, Bin Ma 3*, and Li Wang 3

1 Bioinformatics Solutions Inc., 145 Columbia St. West, Waterloo, Ont. Canada, N2L 3L2
2 School of Computer Science, University of Waterloo, Ont. N2L 3G1, Canada
3 Department of Computer Science, University of Western Ontario, London, Ont. N6A 5B7

* To whom correspondence should be addressed. E-mail: bma{at}csd.uwo.ca.


  Abstract

Summary: New ideas, spaced seeds and gapped alignment before 6-frame translation, are implemented for translated homology search in tPatternHunter. The new software compares favorably over tBLASTx.

Availability: The software is free to the academics at http://www.bioinformaticssolutions.com/downloads/ph-academic/.


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
L. Ilie and S. Ilie
Multiple spaced seeds for homology search
Bioinformatics, November 15, 2007; 23(22): 2969 - 2977.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X. Cui, T. Vinar, B. Brejova, D. Shasha, and M. Li
Homology search for genes
Bioinformatics, July 1, 2007; 23(13): i97 - i103.
[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.