Skip Navigation


Bioinformatics Advance Access originally published online on October 11, 2006
Bioinformatics 2007 23(19):2622-2624; doi:10.1093/bioinformatics/btl513
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
23/19/2622    most recent
btl513v1
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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Bainbridge, M. N.
Right arrow Articles by Jones, S. J.M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bainbridge, M. N.
Right arrow Articles by Jones, S. J.M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

THOR: targeted high-throughput ortholog reconstructor

Matthew N. Bainbridge *, René L. Warren , An He , Mikhail Bilenky , A. Gordon Robertson and Steven J.M. Jones

British Columbia Cancer Agency (BCCA) Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC, Canada

*To whom correspondence should be addressed.


  Abstract

Summary: Low-coverage genomes (LCGs) are becoming an increasingly important source of data for phylogenetic studies. However, assembly of these genomes is time consuming, difficult and lags behind sequence generation. THOR is a fast, stringent application for targeted reconstruction of sequence orthologs in unassembled LCGs. Using a 4x coverage set of mouse whole-genome sequence reads, THOR could partially or completely reconstruct 416/1000 human promoter ortholog regions in ~7.3 min/promoter. THOR's reconstruction rate improves markedly with both higher-coverage, and less divergent target species.

Availability: THOR is implemented in java and is currently available as source code and as a web service (www.bcgsc.ca/services/thor) for reconstructing human sequences.

Contact: matthewb{at}bcgsc.ca

Received on September 21, 2006; accepted on October 26, 2006

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.