Illustration of the alternative transcript similarity scoring scheme. For an orthologue group with two alternative transcripts in each species, a global multiple sequence alignment results in the alignment of homologous exons. Where an alignment of isoforms that differ in the number of exons is used to calculate the similarity score (eg P1-P2') a score <1 will be obtained (0.67 in this case if the exons are assumed to have equal length) as the extra exon is matched by a gap in the alignment. P1-P1' and P2-P2' will give scores of 1.
Jia et al. BMC Genomics 2010 11(Suppl 4):S11 doi:10.1186/1471-2164-11-S4-S11