Motif discovery and motif finding from genome-mapped DNase footprint data.
BACKGROUND
Footprint data is an important source of information on transcription factor recognition motifs. However, a footprinting fragment can contain no sequences similar to known protein recognition sites. Inspection of genome fragments nearby can help to identify missing site positions.


RESULTS
Genome fragments containing footprints were supplied to a pipeline that constructed a position weight matrix (PWM) for different motif lengths and selected the optimal PWM. Fragments were aligned with the SeSiMCMC sampler and a new heuristic algorithm, Bigfoot. Footprints with missing hits were found for approximately 50% of factors. Adding only 2 bp on both sides of a footprinting fragment recovered most hits. We automatically constructed motifs for 41 Drosophila factors. New motifs can recognize footprints with a greater sensitivity at the same false positive rate than existing models. Also we discuss possible overfitting of constructed motifs.


BACKGROUND
Software and the collection of regulatory motifs are freely available at http://line.imb.ac.ru/DMMPMM.
Kulakovskiy
Ivan V
IV
Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. ivan.kulakovskiy@gmail.com
Favorov
Alexander V
AV
Makeev
Vsevolod J
VJ
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D003851:Deoxyribonucleases / Q000737:chemistry*; D004330:Drosophila / Q000235:genetics; D008969:Molecular Sequence Data; D012984:Software
D003851:Deoxyribonucleases