Fig. 1.

Illustration of the graph construction for a gene with 5 exons. The original splicing graph is represented in (a). The 5 exons are represented as vertices and an arrow between two vertices indicates a junction. The nodes of graph $G\prime$ in (b) and (c) are bins with positive effective length denoted by gray square, as well as source s and sink t represented as circles. $G\prime$ in (b) is the resulting graph when all exons are bigger than the read length. In that case, each bin either corresponds to a unique exon, or to a junction between two exons. $G\prime$ in (c) is the resulting graph when the length of exon 3 is smaller than the read length. Some bins involve then more than two exons, here bins $(2\text{-}3\text{-}4)$ and $(2\text{-}3\text{-}5)$. The source links all possible starting bins, and conversely all possible stopping bins are linked to the sink. There is a one-to-one correspondence between (s, t)-paths in $G\prime$ (paths starting at s and ending at t) and isoform candidates. For example, the path $(s,1,1\text{-}4,4,4\text{-}5,5,t)$ corresponds to isoform 1-4-5