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plotcon |
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.
% plotcon -sformat msf alignment.msf
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 This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. Advanced qualifiers: -data boolean Output the match data to a file instead of plotting it General qualifiers: -help boolean 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 | This is the scoring matrix file used when comparing sequences. By default it is the file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These files are found in the 'data' directory of the EMBOSS installation. | 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 |
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:
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 |