Genome-specific higher-order background models to improve motif detection.
Motif detection based on Gibbs sampling is a common procedure used to retrieve regulatory motifs in silico. Using a species-specific background model was previously shown to increase the robustness of the algorithm. Here, we demonstrate that selecting a non-species-adapted background model can have an adverse effect on the results of motif detection. The large differences in the average nucleotide composition of prokaryotic sequences exacerbate the problem of exchanging background models. Therefore, we have developed complex background models for all prokaryotic species with available genome sequences.
Marchal
Kathleen
K
ESAT SISTA-SCD, K.U.Leuven, Kasteelpark Arenberg 10, 3001 Leuven-Heverlee, Belgium. Kathleen.Marchal@esat.kuleuven.ac.be
Thijs
Gert
G
De Keersmaecker
Sigrid
S
Monsieurs
Pieter
P
De Moor
Bart
B
Vanderleyden
Jos
J
D000465:Algorithms; D021901:DNA, Intergenic / Q000032:analysis; D004926:Escherichia coli / Q000235:genetics; D016678:Genome; D023281:Genomics; D008957:Models, Genetic; D011401:Promoter Regions, Genetic; D011550:Pseudomonas aeruginosa / Q000235:genetics; D012045:Regulatory Sequences, Nucleic Acid; D017422:Sequence Analysis, DNA; D012808:Sigma Factor / Q000235:genetics; D013045:Species Specificity
D021901:DNA, Intergenic; D012808:Sigma Factor