Surface plots of poly(A) prediction sensitivities as a function of various PSSMs. (A) Predictions within 10 bases of sequenced poly(A) site when scanning the entire intergenic region (IR) and (B) when limiting scanning to 100 bases upstream of the predicted splice junction. Predictions within 100 bases when scanning the whole IR (C) and constrained by 1000 bases of the predicted splice junction (D). Sensitivities are presented as the average of 15 runs of ten fold cross-validation for each PSSM. The 5' and 3' PSSM size axes correspond to the region upstream and downstream of the genomic alignment of mapped poly(A) sites, respectively. In order to amplify the resolution of regions directly surrounding the poly(A) sites, the scale for 5' and 3' matrix sizes inferior to 100 is decreased from 50 to 25.