Fig 1.
The left side shows pre-processing steps, the right side, post-processing. Input to SCRMshaw consists of the genome sequence and gene annotation. A protein sequence annotation is supplied later for the ortholog mapping step. Adapted from [19].
Fig 2.
Post-processing is described in [14], with modifications in [19]. (A) Scores from each of the 25 individual SCRMshaw instances are assessed and (B) any 500 bp window whose score is below the value of the 5000th ranked score is eliminated by having its score reset to zero (B). (C) The “elbow” point of the SCRMshaw score curve of the 5000 top scores from each instance is then determined, and (D) any scores below the elbow point are reset to zero. (E, F) After these two rounds of score evaluation, windows are grouped together and (G) subjected to peak calling on 10 bp intervals. (H) Final predictions are chosen as peaks with an amplitude above the elbow point of the amplitude curve, represented by a red dot. Adapted from [19].