Differences in number of homologs and reciprocal best hits (RBHs).

<p>All numbers were normalized against the corresponding numbers obtained with NCBI's BLAST. As expected, the faster programs found fewer RBHs than BLAST. Such differences become more evident as the similarity between genomes decreases (as the genomic similarity score, , decreases). This effect was much more pronounced for BLAT. The number of genes finding RBHs (a) and the total RBHs (c) was so small that the two graphs are almost identical. However, the differences between genes finding homologs and the total number of homologous pairs is much more apparent. The number of homolog pairs was always smaller for the fastest programs than for BLAST, suggesting that a good proportion of the differences in RBHs found is due to a lower search depth by the faster programs. See Note in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0101850#pone-0101850-g001" target="_blank">Figure 1</a>.