plotcon reads a sequence alignment and draws a plot of the sequence conservation within windows over the alignment.
Sequence conservation is calculated for windows of a specified length over the alignment. Within a window, the similarity of any one position is taken to be the average of all the possible pairwise substitution scores of the bases or residues at that position. The pairwise substitution scores are taken from the specified similarity matrix. The average of the position similarities within the window is plotted.
The average similarity is calculated by:
Av. Sim. = sum( Mij*wi + Mji*wj )
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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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The program is useful for visualising the quality of alignment along its length. This can give a qualitative insight into where there are regions of conservation in a group of aligned sequences.
Note that you should only compare the results of two runs of plotcon if you use the same window size in each. This is because the 'similarity score' units that are output are very sensitive to the size of the window. A large window (e.g. 100) gives a nice, smooth curve, and very low 'similarity score' units, whereas a small window (e.g. 4) gives a very spikey, noisy plot with 'similarity score' units of a round 1.00
plotcon does not distinguish between aligned and unaligned sets of sequences. If the input set of sequences is unaligned, the output will in most cases lack much biological meaning.