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|Distances between sequences|
It is considered that the space, where all amino acids and
sequences are analysed, is a metric one. It means, a special
measure, named "distance", is entered. It shows, how far (or
how similar) to each other the proteins are. Here, the structural
similarity is considered and, through this, a kind of functional
similarity is explained. Among 20 amino acids there are some
specific (e. g., tryptophan), which are present rather seldom.
Another group of amino acids - aliphatic acids, very often, and,
besides, not very special. It's evidently that these two cases
should be differed.
where S(i,j) is the element of substitution matrix,
placed in the i-th row and the j-th
column. As substitution matrices are symmetrical, obtained distance
matrix is also symmetrical: D(i,j) = D(j,i).
With the help of entered qualities it is easy to express some
parameters of alignments and their positions. Thus, average
distance in position is a measure of homogeny of this
position. Really, the less is the distance between sequences,
the more similar these sequences are, and vice versa. Hence,
the less is the average distance in alignment position, the
more homogenous this position is.
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