Skip Navigation


Bioinformatics Advance Access originally published online on December 14, 2004
Bioinformatics 2005 21(9):2093-2094; doi:10.1093/bioinformatics/bti224
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow All Versions of this Article:
21/9/2093    most recent
bti224v1
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 (5)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Michael, M.
Right arrow Articles by Vingron, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Michael, M.
Right arrow Articles by Vingron, M.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

SITEBLAST–rapid and sensitive local alignment of genomic sequences employing motif anchors

Morris Michael *, Christoph Dieterich {dagger} and Martin Vingron

Computational Molecular Biology, Max Planck Institute for Molecular Genetics Ihnestraße 63–73, D-14195 Berlin, Germany

*To whom correspondence should be addressed.

Motivation: Comparative sequence analysis is the essence of many approaches to genome annotation. Heuristic alignment algorithms utilize similar seed pairs to anchor an alignment. Some applications of local alignment algorithms (e.g. phylogenetic footprinting) would benefit from including prior knowledge (e.g. binding site motifs) in the alignment building process.

Results: We introduce predefined sequence patterns as anchor points into a heuristic local alignment strategy. We extended the BLASTZ program for this purpose. A set of seed patterns is either given as consensus sequences in IUPAC code or position-weight-matrices. Phylogenetic footprinting of promoter regions is one of many potential applications for the SITEBLAST software.

Availability: The source code is freely available to the academic community from http://corg.molgen.mpg.de/software

Contact: christoph.dieterich{at}molgen.mpg.de


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
 DevelopmentHome page
B. Yi and R. J. Sommer
The pax-3 gene is involved in vulva formation in Pristionchus pacificus and is a target of the Hox gene lin-39
Development, September 1, 2007; 134(17): 3111 - 3119.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
A. S. Bais, S. Grossmann, and M. Vingron
Simultaneous alignment and annotation of cis-regulatory regions
Bioinformatics, January 15, 2007; 23(2): e44 - e49.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
C. Dieterich, M. W. Franz, and M. Vingron
Developments in CORG: a gene-centric comparative genomics resource
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D32 - D35.
[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.