SFmap is a computational tool that enables accurate prediction and mapping of known splicing factor binding sites on RNA sequences. In order to accurately map splicing regulatory motifs, SFmap exploits two major attributes of functional binding sites: their propensity to be grouped into clusters of similar motifs and their high evolutionary conservation. SFmap implements the COS(WR) algorithm which computes similarity scores for a given regulatory motif based on information derived from its sequence environment. These scores are calculated in two steps: first, the Weighted Rank (WR) function is applied to calculate the clustering propensity of the motif. Second, the evolutionary conservation is estimated by further weighting the WR scores with the Conservation Of Score (COS) function. The COS function relaxes positional constrains imposed by sequence alignments therefore it is ideal for estimating the evolutionary conservation of regulatory motifs.
For more detailed information about SFmap algorithm, read: Akerman et al., 2009.
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