Fig. 3.

Sensitivity and specificity comparisons of Trans-ABySS and ASplice with respect to alternative splicing junctions in model organisms over different values of k and k-mer coverage cutoff c (represented by k_c). Sensitivity (sens; marked by bars) is defined to be the percentage of junctions in the gene transcripts that appear in the assembly. Specificity (spec; marked by lines) is defined to be the percentage of junctions in the assembly that appear in the gene transcripts. Junctions in the gene transcripts are defined by concatenating the two sequences of length k that are immediately to the left and immediately to the right of all locations with alternative splicing that are derived from annotated positions of the gene transcripts to obtain a sequence of length 2k. Junctions in the assembly are defined by concatenating the two non-overlapping k-mers at the beginning and ending nodes of an edge to obtain a sequence of length 2k. Up to three mismatches are allowed when looking for occurrences of these sequences that span across a junction. Notations are the same as in Fig. 2