Figure 6

Comparisons of the alternative splicing junction results in the simulated transcriptome assemblies of Drosophila using its known complete genome over different values of k and k -mer coverage cutoff c (represented by k_c ) with varying percentages of mismatches in the reads. Sensitivity is defined to be the percentage of junctions in the gene transcripts of Drosophila that appear somewhere in the assembly. Specificity is defined to be the percentage of junctions in the assembly that appear somewhere in the gene transcripts of Drosophila. Junctions in the gene transcripts of Drosophila are defined by concatenating the two sequences of length k that are immediately to the left and immediately to the right of all alternative splicing locations to obtain a sequence of length 2k. Junctions in the assembly are defined by concatenating the two k-mers at the beginning and ending nodes of an edge to obtain a sequence of length 2k after the elimination of overlapping sequence fragments between adjacent nodes. Up to three mismatches are allowed when looking for these sequence occurrences.