Figure 1.

Pipeline of splice alignment. Splice alignment contains six steps. We use trichotomy as divide method, three equal segments are regarded as seeds and finish unspliced mapping by BWA - an unspliced aligner. Segments results are filtered based on the mapping results and known splice junctions' information. Then, we try to search splice sites based on mapped segments information and known splicing motifs. Splice alignment will be finished after segments extension, and all splice sites are recorded. Gapped alignment is allowed in both initial alignment stage and heuristic alignment stage.