Finally, a supervised search of "+" intergenic regions is performed, so as to insure that all copies of the motif identified by the pairwise alignment are detected.
Significant similarity of DNA sequences in small, gapless alignments were detected by manual inspection of results from GLAM [ 55], followed by alignment of larger regions, with gaps, by Clustal W or MUSCLE.
We replicated this procedure a 1000 times and, then, asked how many times each of the pairs of sites detected as coevolving in the real multiple sequence alignments was detected as significantly supporting coevolution.
Conserved positions in the alignments were detected using BMGE with default parameters and the BLOSUM62 substitution matrix, which represents a good compromise between too stringent and too relaxed matrices to deal with sequences with a large range of similarity values as in the case of global archaeal phylogenies (Criscuolo and Gribaldo 2010).
As such, we advocate an approach whereby once measurement non-invariance (under full, classical partial or with alignment framework) is detected, in-depth analyses are necessary to locate its source.
Usually, regions of ambiguous alignment (RAA) are detected by alignment inspection and then discarded.
Only subtle alignments could be detected in the immediate vicinity of the ablated zone in large-scale lacerations, but no alignment over several cell files was observed.
In contrast to classical techniques such as the Hough transforms, which are designed for detecting a specific type of alignment on a given type of input, our approach is independent of the geometric properties of the alignments to be detected, as well as independent of the type of input data.
These alignments can be detected even when the DNA sequence is too divergent to align easily.
Local-alignment anchors were detected using PatternHunter (1e-10) [ 41].
