plotcon

Function

Description

Displays a graphical representation of the similarity along a set of aligned sequences.

The similarity is calculated by moving a window of a specified length along the aligned sequences. Within the window, the similarity of any one position is taken to be the average of all the possible pairwise scores of the bases or residues at that position. The pairwise scores are taken from the specified similarity matrix. The average of the position similarities within the window is plotted.

The program is useful for determining where the quality of alignments is good or bad.

The average similarity is calculated by:

Av. Sim. =       sum( Mij*wi + Mji*wj  )
                      -------------------
                  (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

This program is useful for gaining 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

Usage

Command line arguments


Input file format

plotcon reads a set of gapped, aligned sequences.

Output file format

A graph of the quality of the alignment is dispalyed on the specifed graphics device.

Data files

It reads in the specified similarity matrix.

Notes

None.

References

None.

Warnings

If you give it a set of unaligned sequences, it will plot the (poor!) quality of these as if they were aligned.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Author(s)

History

Target users

Comments