At higher conservation levels the CBW&DMS algorithms together do not outperform DMS alone, though both do better than BW or CBW alone.
We also looked at the high conservation of at least one residue in each transmembrane helical segment (see above).
For example, in conservation analysis, gaps in alignment are frequently treated as missing data when computing conservation scores [ 49], but misalignments are less likely to occur at regions of high conservation [ 50] (Additional file 1: Fig. S9).
It is frequently observed that there is high conservation at coding regions and lower conservation at noncoding regions (for example, see Figure S2A).
We do not yet know the reasons for these differences, nor whether high conservation at one scale (e.g., genetic map) in any way correlates with high conservation at other scales (e.g., physical map or microcolinearity).
At exon 7, although high conservation across non-bats was confirmed [4], we also found previously unreported single amino acid changes in two eulipotyphlan insectivores (Ala283), pig (Asp280) and, the goat (Thr315), though the latter of these was also previously found in the cow [4].
However, both models show high conservation at many positions and a marked signal for hydrophobicity.
EST-SSR amplicons showed high conservation at the flanking SSR regions of both Lupinus species when compared with L. luteus.
The trade-off between groEL´s high conservation at the sequence and functional levels and its high propensity to evolve novel functions remains poorly understood.
A comparison of the translated H3 open reading frame with the published database of histone sequences [ 51] confirmed high conservation at the level of amino acids.
