Figure 4.

Evaluation of BPS and PPT profile models. Sequence logos representing each BPS and PPT profile model [Weblogo (29)] are shown with statistics for each model: ‘% of Introns with Above Threshold Matches’ is the percent of introns with any profile match above threshold (‘Materials and Methods’ section) in the entire intronic region from −199 to +1; ‘% of Above-Background Best Matches in Expected Region’ was determined by first calculating an average background level of best matches at each position in the range from −189 to −90 from the 3′-splice site, subtracting this background value from number of best matches at each position, and comparing the number of these residual best matches in the expected BPS region (BP A in −45 to −16) or PPT region (5′-PPT start of match in the region from −30 to −11) to the number of expected background matches in the expected region (‘Materials and Methods’ section); ‘Signal-to-Noise Ratio’ is the improvement over random based on the residual number of best matches in the expected region relative to the background estimate; ‘Correlation with SF1 Affinity’ is the Pearson correlation coefficient between profile model bit scores and SF1 affinities for the 46 sequences assayed.