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PLOTCON application details page
Plots the quality of conservation of a sequence alignment
Displays a graphical representation of the similarity along a set of aligned sequences. The similarity is calculated by moving a window of a specified lengthalong the aligned sequences. Within the window, the similarity of anyone position is taken to be the average of all the possible pairwisescores of the bases or residues at that position. The pairwise scoresare taken from the specified similarity matrix. The average of theposition similarities within the window is plotted. The program is useful for determining where the quality of alignmentsis good or bad. The average similarity is calculated by: Av. Sim. = sum( Mij*wi + Mji*w2 )
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(Nseq*Wsize)*((Nseq-1)*Wsize)sum - over column*window size
w - sequence weighting
M - matrix comparison table
i,j - with respect to residue i or j
Nseq - number of sequences in the alignment
Wsize - window size
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