Selection of Putative Cis-regulatory Motifs through Regional and Global Conservation

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TypeArticle
ConferenceSystems Bioinformatics Conference (CSB2004), August 16-19, 2004., Stanford, California, USA
AbstractCis-regulatory motifs are often overrepresented in promoters and may exhibit frequency biases in subpromoter regions (SPRs). Many probabilistic algorithms have been used to predict such motifs, but they tend to generate many false positives. We devised a novel algorithm, MotifFilter, that computes Representation Indices (RIs) for putative motifs. MotifFilter's RI is a ratio of the actual over expected frequency of a motif in promoters, SPRs or random genomic DNA that takes into account of the nucleotide probability distributions in these regions. This approach was applied to a genome-wide survey of putative cAMP-response elements (CREs) for motifs generated by a profile hidden Markov model. Twenty of 144 putative CRE motifs found in the survey were retained by the MotifFilter.
Publication date
LanguageEnglish
AffiliationNRC Institute for Information Technology; National Research Council Canada
Peer reviewedNo
NRC number47133
NPARC number5764633
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Record identifier7050a2dd-f5e9-468b-92c2-d24c57da2df8
Record created2009-03-29
Record modified2016-06-01
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