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Fig. 2 | BMC Bioinformatics

Fig. 2

From: ASGAL: aligning RNA-Seq data to a splicing graph to detect novel alternative splicing events

Fig. 2

Precedence relation between MEMs. Two MEMs, m=(iZ,iR,l) and \(m^{\prime } = \left (i^{\prime }_{Z}, i^{\prime }_{R}, l^{\prime }\right)\), are shown in the figure. For ease of presentation we represent in blue the former and in red the latter. Since \(i_{Z} < i^{\prime }_{Z}\) and \(i_{Z} + l < i^{\prime }_{Z} + l^{\prime }\), m precedes m on Z; analogously m precedes m on R since \(i_{R} < i^{\prime }_{R}\) and \(i_{R} + l < i^{\prime }_{R} + l^{\prime }\). The length lgapZ of the gap between the two MEMs on Z is positive and we refer to the string between iZ+l and \(i^{\prime }_{Z} - 1\) as sgapZ (highlighted in yellow). Conversely, the length of the gap between the two MEMs on R is negative and we say that they overlap on R. Finally, we refer to the string between the start of the vertex label and iZ−1 as PREFZ(m) (highlighted in light blue), and to the string between \(i^{\prime }_{Z} + l\) and the end of the vertex label as SUFFZ(m) (highlighted in light red). For ease of presentation, we did not report SUFFZ(m) and PREFZ(m)

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