Position-dependent motif characterization using non-negative matrix factorization.
Ontology highlight
ABSTRACT:
SUBMITTER: Hutchins LN
PROVIDER: S-EPMC2639279 | biostudies-literature | 2008 Dec
REPOSITORIES: biostudies-literature
Publications
Position-dependent motif characterization using non-negative matrix factorization.
Hutchins Lucie N LN Murphy Sean M SM Singh Priyam P Graber Joel H JH
Bioinformatics (Oxford, England) 20081013 23
<h4>Motivation</h4>Cis-acting regulatory elements are frequently constrained by both sequence content and positioning relative to a functional site, such as a splice or polyadenylation site. We describe an approach to regulatory motif analysis based on non-negative matrix factorization (NMF). Whereas existing pattern recognition algorithms commonly focus primarily on sequence content, our method simultaneously characterizes both positioning and sequence content of putative motifs.<h4>Results</h4 ...[more]
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