Jaccard index based similarity measure to compare transcription factor binding site models.

ABSTRACT:

Background

Positional weight matrix (PWM) remains the most popular for quantification of transcription factor (TF) binding. PWM supplied with a score threshold defines a set of putative transcription factor binding sites (TFBS), thus providing a TFBS model.TF binding DNA fragments obtained by different experimental methods usually give similar but not identical PWMs. This is also common for different TFs from the same structural family. Thus it is often necessary to measure the similarity between PWMs. The popular tools compare PWMs directly using matrix elements. Yet, for log-odds PWMs, negative elements do not contribute to the scores of highly scoring TFBS and thus may be different without affecting the sets of the best recognized binding sites. Moreover, the two TFBS sets recog

SUBMITTER: Vorontsov IE 

PROVIDER: S-EPMC3851813 | biostudies-literature | 2013 Sep

REPOSITORIES: biostudies-literature