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Bioinformatics Advance Access published online on November 8, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl551
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received September 5, 2006
Accepted October 19, 2006

Applications note

Pattern Locator: a new tool for finding local sequence patterns in genomic DNA sequences

Jan Mrázek 1 * and Shaohua Xie 2

1 Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
2 Department of Computer Science, University of Georgia, Athens, GA 30602, USA

* To whom correspondence should be addressed.
Jan Mrázek, E-mail: mrazek{at}uga.edu


  Abstract

Summary: We present a new tool for finding local sequence patterns in long DNA sequences. The program, Pattern Locator, uses an intuitive syntax for pattern description, and provides more flexibility than existing programs by allowing combinations of specific nucleotide sequences, direct and inverted repeats, variable length tandem repeats of any subpatterns, and a specified number of errors in any part of the pattern.

Availability: The program is available for download and as a web service accessible through a CGI interface at http://www.cmbl.uga.edu/software.html. The source code is written in C and distributed under the GNU General Public License.

Associate Editor: Limsoon Wong
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