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Bioinformatics Advance Access published online on February 12, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth094
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received April 15, 2003
Revised December 10, 2003
Accepted January 6, 2003

Applications note

Site2genome: locating short DNA sequences in whole genomes

Martin C. Frith 1, Anason S. Halees 1, Ulla Hansen 2, Zhiping Weng 3*

1 Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA
2 Biology Department, Boston University, 44 Cummington Street, Boston, MA 02215, USA
3 Bioinformatics Program, Boston University, 44 Cummington Street, Boston, MA 02215, USA; Biomedical Engineering Department, Boston University, 44 Cummington Street, Boston, MA 02215, USA

* To whom correspondence should be addressed. E-mail: zhiping{at}bu.edu.


  Abstract

Summary: Many biological papers describe short, functional DNA sites without specifying their exact positions in the genome. We have developed a web server that automates the tedious task of locating such sites in eukaryotic genomes, thus giving access to the context of rich annotations that are increasingly available for genome sequences.

Availability: http://zlab.bu.edu/site2genome/


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