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Bioinformatics Advance Access published online on June 20, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl330
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received March 16, 2006
Revised May 23, 2006
Accepted June 9, 2006

Applications note

Cleaver: software for identifying taxon specific restriction endonuclease recognition sites

Simon N. Jarman 1 *

1 Department of the Environment and Heritage, Australian Antarctic Division, 203 Channel Highway, Kingston, TAS, 7050, Australia

* To whom correspondence should be addressed.
Simon N. Jarman, E-mail: simon.jarman{at}aad.gov.au


  Abstract

Summary: Cleaver is an application for identifying restriction endonuclease recognition sites that occur in some taxa but not in others. Differences in DNA fragment restriction patterns among taxa are the basis for many diagnostic assays for taxonomic identification; and are used in some procedures for removing the DNA of some taxa from pools of DNA from mixed sources. Cleaver analyses restriction digestion of groups of orthologous DNA sequences simultaneously to allow identification of differences in restriction pattern among the fragments derived from different taxa.

Availability: Cleaver is freely available without registration from its website (http://cleaver.sourceforge.net/) and can be copied, modified and re-distributed under the terms of the GNU general public licence version2 (http://www.gnu.org/licences/gpl). The program can be run as a script for computers that have Python 2.3 and necessary extra modules installed. This allows it to run on Gnu/Linux, Unix, MacOSX and Windows platforms. Standalone executable versions for Windows and MacOSX operating systems are available.

Associate Editor: Golan Yona
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