Fig. 1.

The transcriptome (consisting of transcripts $t_1,\dots ,t_6$) is converted into a $\$$-separated string, T, on which a suffix array, SA[T], and a hash table, h, are constructed. The mapping operation begins with a k-mer (here, k = 3) mapping to an interval $\left[b,e\right)$ in SA[T]. Given this interval and the read, MMP_i and NIP(MMP_i) are calculated as described in section 2. The search for the next hashable k-mer begins k bases before NIP(MMP_i)