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Updated: Jun 21, 2026
DNA-affinity-purified Chip (DAP-chip) Method to Determine Gene Targets for Bacterial Two component Regulatory Systems
Published on: July 21, 2014
Motif discovery and motif finding from genome-mapped DNase footprint data
Ivan V Kulakovskiy1, Alexander V Favorov, Vsevolod J Makeev
1Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. ivan.kulakovskiy@gmail.com
Motivation:
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.
Availability:
Software and the collection of regulatory motifs are freely available at http://line.imb.ac.ru/DMMPMM.
