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Briefings in Bioinformatics Advance Access originally published online on June 24, 2009
Briefings in Bioinformatics 2009 10(5):525-536; doi:10.1093/bib/bbp032
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© The Author 2009. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Finding sequence motifs in prokaryotic genomes—a brief practical guide for a microbiologist

Jan Mrázek

Corresponding author. Department of Microbiology and Institute of Bioinformatics, University of Georgia, Athens, GA 30602-2605, USA. Tel: +1 706-542-1065; Fax: +1 706-542-2674; E-mail: mrazek{at}uga.edu

Finding significant nucleotide sequence motifs in prokaryotic genomes can be divided into three types of tasks: (1) supervised motif finding, where a sample of motif sequences is used to find other similar sequences in genomes; (2) unsupervised motif finding, which typically relates to the task of finding regulatory motifs and protein binding sites and (3) exploratory motif finding, which aims to identify potential functionally significant sequence motifs as those that are unusual in some statistical sense. This article provides a conceptual overview for each type of task, a brief description of basic algorithms used in their solution, and a review of selected relevant software available online.

Keywords: supervised motif finding, unsupervised motif finding, phylogenetic footprinting, r-scan statistics, protein binding sites, software review

Submitted: March 13, 2009. Received (in revised form): June 3, 2009.


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