The orthology relationship. A. Design of the orthology relationship. Step 1 : Two reciprocal TBLASTX for comparing species A and species B transcript sequences. Step 2 : We conserve only the pairs of transcript sequences originating consistent TBLASTX(1) and TBLASTX(2) results. Step 3 : We consider previously obtained pairs in order to limit erroneous assignment of orthologous pairs for paralogous ones. B. The best reciprocal TBLASTX hits might correspond to paralogs. This figure provides an example of a phylogenetic tree where the best reciprocal TBLASTX hits correspond to paralogs because several transcript sequences are unknown (represented with dotted lines). To avoid such erroneous assignment of orthologous pairs we followed reciprocal best BLAST by another step (figure 3A, step 3) considering that even if the transcript sequences A1 and B2 are unknown, one of their corresponding proteins might be in a protein databank.
Keime et al. BMC Bioinformatics 2004 5:143 doi:10.1186/1471-2105-5-143