Fig. 7
From: ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events
Conditions for linking two different MEMs. All the conditions used to connect two different MEMs and then to build the factors and gap-factors of a spliced graph-alignment are shown. In all the conditions, the first MEM must precede the second one on the read. In condition (a) and (b), the two MEMs occur inside the same vertex label and leave a gap (condition a) or overlap (condition b) on the read or on the vertex label. In these conditions, the two MEMs are joined in the same factor of the alignment. In condition c, instead, the two MEMs occur inside the same vertex label but they leave a long gap only on the vertex label and not on the read. In this case, the two MEMs belong to two different factors linked by a gap-factor. In the other conditions, instead, the two MEMs are inside the labels of two different vertices of the splicing graph, linked by a (possible novel) edge. For this reason, in any of these cases, the two MEMs belong to two different factors of the alignment. In condition d, the two MEMs leave a gap only the path, in condition e they leave a gap only on the read, and in condition f, they leave a gap on both the path and the read