2. On page 6 there is a reference to HMM searches initiated with models built from multiple alignments; however, there is no mentioning of the HMMER package in the Materials and Methods.
The multiple alignment shows, however, that the amino acid sequences on both sides of the frameshift have retained strong similarity to closely and distantly related homologs.
Existing RNA-seq analysis pipelines provide heuristics for addressing the multiple alignment problem, however, they do not explicitly consider their genomic causes.
It might then seem that rather than BLASTZ, a better comparison of Murasaki would be to a natively "multiple" alignment program like Mauve; however it is important to note that Murasaki performs a fundamentally different function than Mauve in that Mauve aligns whole collinear regions bounded by unique anchors.
The GOS 6800 CP sequence is truncated and was thus not used in the multiple alignment or phylogenetic analysis, however the available sequence was sufficient for BLASTp comparison.
PSI-BLAST searches failed to identify reliable similarity of COG2929 proteins to any characterized proteins; however, the multiple alignment includes several conserved positions occupied by polar residues which is compatible with an enzymatic activity of the COG2929 family proteins.
However, DIALIGN uses a greedy approach only for multiple alignment where an exact solution is not feasible, but for pairwise alignment, the program returns an optimal alignment with respect to the underlying objective function.
However, diverse strategies for seeds detection cause a distinction among multiple alignment algorithms.
However, the 8 CM C-terminal domains are conserved enough to allow multiple alignment construction and phylogenetic analyses.
However, in practice, estimators based on the E-value of the resulting multiple alignment are used instead [ 4].
