Building the fusion junction sequence library using a partial exhaustion algorithm. A junction sequence in a fusion transcript from a gene pair, Gene A and Gene B in blue and orange, respectively, is shown. The junction site is shown as yellow round dots on the fusion segment, and as yellow triangles on the gene pair. (a) Fused regions 1 and 2 from two different methods are shown and fused region 2 is divided into credible-regions and potential-regions with the coordinates of each sub-region labeled in red font. An upstream putative junction site (Ui) is selected from fused region 2 in Gene A, and a downstream putative junction site (Dj) is selected from fused region 2 in Gene B. (b) For each Ui and Dj, SOAPfuse generates the candidate fusion junction sequence by creating pair-wise connections between Ui and Dj . Ui and Dj should not be located in potential-regions at the same time.
Jia et al. Genome Biology 2013 14:R12 doi:10.1186/gb-2013-14-2-r12