Transcription factor binding site detection through position cross-mutual information variability analysis.
Regulatory sequence detection is a fundamental challenge in computational biology. One key process in protein synthesis starts with the binding of the transcription factor to its binding site. Different sites can show binding to the same factor. This variability found in binding sequences increases the difficulty of their detection using computational algorithms. In this manuscript, a method for the detection of binding sites is proposed, based on the correlation between binding sequence positions through information theoretical measures. Efficiency values of the method are reported in the form of Receiver Operating Characteristic curves on the detection of different transcription factors of the Saccharomyces cerevisiae organism. We compare our results with other known motif detection Motif Discovery scan (MDscan).
Maynou
Joan
J
Dep. ESAII, Centre for Biomedical Engineering Research, Technical University of Catalonia (UPC), Barcelona, Gargallo, 5, 08028 Barcelona, Spain. joan.maynou@upc.edu
Vallverdu
Montserrat
M
Claria
Francesc
F
Gallardo-Chacon
Joan-Josep
JJ
Caminal
Pere
P
Perera
Alexandre
A
D000465:Algorithms; D001665:Binding Sites / Q000235:genetics; D001698:Biomedical Engineering; D004268:DNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D012372:ROC Curve; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
C061886:ABF1 protein, S cerevisiae; D004268:DNA-Binding Proteins; D029701:Saccharomyces cerevisiae Proteins; D014157:Transcription Factors