The occurrence of recombination events within homologous sequences can also significantly interfere with reliable GSPSD, since the codon evolution models commonly used to detect positive selection do not take into account recombination as a possible source of variation of homologous positions and assume all the columns of a multiple codon alignment to share the same evolutionary story [ 20].
HMMs were built from highly curated multiple alignments of proteins thought to share the same function or to be members of the same protein family.
All of the proteins from the genome sequence were also searched against the Pfam [39] (release 20.0) HMMs (hmmpfam HMMER version 2.3.2, parameters: -E 0.1 –cut_ga) and TIGRFAMs [40] (release 6.0) built from highly curated multiple alignments of proteins thought to share the same function or to be members of the same family.
However, previous approaches to aligning gene-expression time series have assumed that all genes should share the same alignment.
At the fourth line in this algorithm, two candidate segments are considered similar if (1) they share the same alignment, (2) they have similar font-size, or (3) the space between them is less than a threshold.
No sections of US 281 were removed from the State Highway System as a result of the construction of I-37, but the two do share the same alignment at two different points between San Antonio and Three Rivers.
To evaluate the robustness of our method against the bias induced by rate heterogeneity, we simulated a 256 bp alignment with eight taxa where all sites share the same topology (first topology in Figure 2A).
We therefore hypothesized that the KO-families within the boundaries of the alignment landscapes of parental/non-parental KO-families share the same or highly related EC hierarchies.
Of these reciprocal hits, 6,942 sequences had alignments where 100% of the 'Prestige' transcript length aligned to the '378' transcript, or vice versa; these transcripts share the same protein length and sequencing reads covered the entire sequence length.
These usually share the same chemical representation library, but full alignment between them is not always certain.
