The good blast score is due to alignments that are longer between the eukaryotic tubulins and the Nitrosoarchaeum sequences.
In such situations, improved optimisation algorithms may lead not only to mathematically higher-scoring alignments but also to alignments that are closer to the biologically correct alignment.
However, the same methodology that provides for the sensitive identification of homology at low identity can also lead to alignments that include non-homologous sequence adjacent to, or between, higher identity homologous sequences (Gonzalez and Pearson, 2010a).
Therefore, to ensure that the pairs of homologous genes implied by these BLAST alignments were indicative of true pairs (as opposed to alignments that could occur simply by random chance), we used three filters: an E-value threshold of 10-6, alignmentent coverage requirement, and the requirement that the alignment was to a gene with assigned function.
Although we cannot rule out this possibility, we feel our strategy prioritized the "optimal" BLAST result among multiple hits for a single marker leading to alignments that agree with nearby unambiguous results (Table 1).
"The electronic distance that lets men write so freely is akin to their preferred way of speaking -- without a direct face-to-face alignment that makes a lot of men uncomfortable," said Dr. Deborah Tannen, a professor of linguistics at Georgetown University and a pioneer in the field of sex differences in language.
The 104 alignments were then concatenated, leading to an alignment that was 39,926 residues long.
The tool also automatically builds models according to the alignment that is being inspected (without modeling insertions) and allows the quantitative assessment of their global and local quality.
Sequences were aligned using MUSCLE v3.8.31; the relatively small number of apparent insertion/deletion events led to an alignment that was <0.3% gap.
Based on a small proportion of MeSH to VCM alignment that had already been manually validated, three inter-alignment consistency measures were used: crude concordance and two measures based on Dice index, with or without semantics.
