MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data.
CONCLUSIONS
Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.


BACKGROUND
MOTIFATOR is freely available at http://www.motifator.nl.
Blom
Evert-Jan
EJ
Molecular Genetics, Groningen Biomolecular Sciences, University of Groningen, PO Box 800, 9700 AV Groningen, The Netherlands.
Roerdink
Jos B T M
JB
Kuipers
Oscar P
OP
van Hijum
Sacha A F T
SA
D017124:Conserved Sequence; D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011387:Prokaryotic Cells; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D012984:Software