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If matches between two sequences are to be found, the situation is slightly more complicated.
The two main factors that favour the occurrence of gene conversion between two sequences are their genomic proximity [ 24], and their degree of sequence homology.
An example of the parsing process to identify the exhaustive history of a sequence and the calculation of the similarity score between two sequences are given below.
Our simulation experiments have revealed that distance between two CVs is proportional to traditional evolutionary distance when substitutions between two sequences are rare (data not shown).
This method assesses whether the nucleotide differences found between two sequences are randomly distributed along the length of these sequences; it cannot detect gene conversions if a given region has fewer differences than its flanking regions.
EX is a directional measure (i.e., EXij≠EXji), and it is therefore particularly useful in phylogenetic studies, in which substitutions observed between two sequences are polarised by the known ancestral state.
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And the last, conclusions are provided in Section 6. Notations: In this paper, the correlation between two sequences is referred to periodic correlation if not specifically pointed out; and we will use upper (lower) boldface letters to denote matrix (column vectors).
The overall pairwise similarity between two sequences is defined as the minimum of these two scores.
The distance between two sequences is the mean of distances between those two sequences in the trees in which both sequences appeared.
The similarity between two sequences is determined by comparing the degree of word overlap between two profiles with the expected overlap given the number of words in each sequence.
After trajectory is smoothened, the search of large-scale correlations between two sequences is done by calculation of two measures: the measure of closeness and the measure of complexity of two curvilinear trajectories.
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