Figure 2

The shortest path model for the optimization of alignment-combinations. Exon i (i = 1…N) in AG are aligned to maybe multiple similar regions in UG. For example, Exon 1 is mapped to Chr1:A ₁ -B ₁ ; … ;Chr2:C ₁ -D ₁ ; …, where Chr1:A ₁ -B ₁ means Exon 1 is aligned from A ₁ to B ₁ in Chromosome 1 of UG. All alignments of Exon i is denoted as stage A _i , and the j ^th alignment of Exon i is denoted as A _i,j . d(A _i,k , A _i + 1,p ) measures the quality of Alignment A _i,k and the rationality of relationship between A _i,k and A _i+1,p for neighbour Exon i and Exon i + 1. The stages “start” and “end” are the beginning and termination of one exon-combination path. The state “skip” is an extra state for each exon-alignment stage for the cases that there is no reasonable alignment available for one certain exon.