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Figure 2 | BMC Bioinformatics

Figure 2

From: Proteinortho: Detection of (Co-)orthologs in large-scale analysis

Figure 2

Adaptive RBAH. Reciprocal best alignment heuristic (RBAH). (a) If there is a pair of divergent co-orthologs x1, , and y1 and , resp., it is possible that there are no reciprocal best blast alignments. In this situation, RBAH will not identify any orthologs. (b) One possible remedy is to include the second best blast alignment (n = 2). However, in this case highly similar orthologs (x2 and y2 as well as x3 and y3), which in principle can clearly be divided, can get combined. (c) Proteinortho uses an adaptive approach that is (1) flexible with respect to the number of more diverged orthologs in absence of a reciprocal best blast alignment and (2) will not intermix orthologous groups that can be disentangled easily because of large differences in pairwise similarity.

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