KIRMES: kernel-based identification of regulatory modules in euchromatic sequences.
BACKGROUND
Understanding transcriptional regulation is one of the main challenges in computational biology. An important problem is the identification of transcription factor (TF) binding sites in promoter regions of potential TF target genes. It is typically approached by position weight matrix-based motif identification algorithms using Gibbs sampling, or heuristics to extend seed oligos. Such algorithms succeed in identifying single, relatively well-conserved binding sites, but tend to fail when it comes to the identification of combinations of several degenerate binding sites, as those often found in cis-regulatory modules.


RESULTS
We propose a new algorithm that combines the benefits of existing motif finding with the ones of support vector machines (SVMs) to find degenerate motifs in order to improve the modeling of regulatory modules. In experiments on microarray data from Arabidopsis thaliana, we were able to show that the newly developed strategy significantly improves the recognition of TF targets.


BACKGROUND
The python source code (open source-licensed under GPL), the data for the experiments and a Galaxy-based web service are available at http://www.fml.mpg.de/raetsch/suppl/kirmes/.
Schultheiss
Sebastian J
SJ
Friedrich Miescher Laboratory of the Max Planck Society, and Max Planck Institute for Developmental Biology, Tübingen, Germany. sebi@tuebingen.mpg.de
Busch
Wolfgang
W
Lohmann
Jan U
JU
Kohlbacher
Oliver
O
Rätsch
Gunnar
G
D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D022041:Euchromatin / Q000737:chemistry*; D011401:Promoter Regions, Genetic; D012984:Software; D014157:Transcription Factors / Q000737:chemistry
D022041:Euchromatin; D014157:Transcription Factors