| ## EMBOSS: plotcon

# Program plotcon

## Function

Plots the quality of conservation of a sequence alignment

## 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.

## Usage

Here is a sample session with plotcon:

    % plotcon -sformat msf alignment.msf

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-msf]               seqset     File containing a sequence alignment
       -winsize            integer    Number of columns to average alignment
                                      quality over. The larger this value is, the
                                      smoother the plot will be.
    *  -graph              xygraph    Graph type
    *  -outfile            outfile    Display as data

       Optional qualifiers:
       -scorefile          matrix     Comparison matrix file

       Advanced qualifiers:
       -data               bool       Output the match data to a file instead of
                                      plotting it

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence alignment | Readable sequences | Required
-winsize | Number of columns to average alignment quality over. The larger this value is, the smoother the plot will be. | Any integer value | 4
-graph | Graph type | EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png | EMBOSS_GRAPHICS value, or x11
-outfile | Display as data | Output file | <sequence>.plotcon
Optional qualifiers | Allowed values | Default
-scorefile | Comparison matrix file | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA
Advanced qualifiers | Allowed values | Default
-data | Output the match data to a file instead of plotting it | Yes/No | No

## Input file format

A set of gapped, aligned sequences.

## Output file format

A graph of the quality of the alignment is plotted.

## Data files

It reads in the specified similarity matrix.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

    % embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:

    % embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## 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.

## See also

Program name | Description
--- | ---
emma | Multiple alignment program - interface to ClustalW program
infoalign | Information on a multiple sequence alignment
prettyplot | Displays aligned sequences, with colouring and boxing
showalign | Displays a multiple sequence alignment
tranalign | Align nucleic coding regions given the aligned proteins

## Author(s)

This application was written by Tim Carver (tcarver@hgmp.mrc.ac.uk)

## History

Written (Sept 2000) - Tim Carver.

## Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

## Comments