Poorly conserved regions of the protein were omitted from the phylogenetic analysis, so that the alignment consisted mostly of TMRs and each sequence had an average of 149 amino acids out of 266 positions in the alignment.
Alignment accuracy, mostly measured in terms of correct residue pairs, has been assessed in many previous studies (Kemena and Notredame, 2009) and has not been the purpose of this work.
Relatedness of vcrABC -cargo sequences was estimated based on the 44 variant positions in their alignment, appearing mostly (66%) in the form of substitutions in the leader sequence of vcrA [ 5].
Despite the large differences in the length of the combined sequence between the two alignment methods (mostly due to LSU), the changes in the topology or level of support of the resulting trees were negligible (see below).
Although we considered best-case similarity between any two conceptually translated long open reading frames (see Materials and Methods), we found that codon substitution patterns do not support the hypothesis of protein-coding ability, as the Ka/Ks ratios for these alignments are mostly in the range 0.5 1.5.
The gene structures derived from cross-species ESTs and Mt ESTs alignments were mostly consistent, demonstrating the value of cross-species ESTs in genome annotation [ 10].
Existing methods for obtaining the optimal alignments are mostly based on an exhaustive scanning of all but discrete relative rigid transformations (i.e. rotations and translations) of one subtomogram with respect to the other.
The problem is analogous to having some of the alignment columns contain mostly gaps: these should be identified as "insertion columns"; in the profile HMM context, there should not be a match state associated with such columns (there should be an insertion state instead).
As topsy-turvy as the Obama-Clinton race has seemed at times, the demographic alignments have been mostly static.
MT amino acid sequences used for pulmonate MT alignments were derived mostly from amino acid sequence files or translated cDNA open reading frame sequences published in GenBank (http://www.ncbi.nlm.nih.gov/Tools/; see accession numbers in the legend to Figure 9).
