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EMBOSS: prettyplot |
% prettyplot $EMBOSS_DATA/globin.msf -resbreak=10 -boxcol -consensus -plurality=3click here for result
$ prettyplot $EMBOSS_DATA/globin.msf -plurality=3 -docolourclick here for result
Mandatory qualifiers (* if not always prompted): [-msf] seqset File containing a sequence alignment * -graph graph Graph type Optional qualifiers: -residuesperline integer The number of residues to be displayed on each line -resbreak integer Residues before a space -[no]ccolours bool Colour residues by their consensus value. -cidentity string Colour to display identical residues (RED) -csimilarity string Colour to display similar residues (GREEN) -cother string Colour to display other residues (BLACK) -docolour bool Colour residues by table oily, amide etc. -[no]title bool Do not display the title -shade string Set to BPLW for normal shading so for pair = 1.5,1.0,0.5 and shade = BPLW Residues score Colour 1.5 or over....... BLACK (B) 1.0 to 1.5 ....... BROWN (P) 0.5 to 1.0 ....... WHEAT (L) under 0.5 ....... WHITE (W) The only four letters allowed are BPLW, in any order. -pair string Values to represent identical similar related -identity integer Only match those which are identical in all sequences. -[no]box bool Display prettyboxes -boxcol bool Colour the background in the boxes -boxcolval string Colour to be used for background. (GREY) -consensus bool Display the consensus -[no]name bool Display the sequence names -maxnamelen integer Margin size for the sequence name. -[no]number bool Display the residue number -[no]listoptions bool Display the date and options used -plurality float Plurality check value (totweight/2) -[no]collision bool Allow collisions in calculating consensus -alternative integer Use alternative collisions routine 0) Normal collision check. (default) 1) checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred. 2) If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. 3) Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured. -portrait bool Set page to Portrait -matrixfile matrix Matrix file -showscore integer Print residue scores Advanced qualifiers: -data bool (no help text) bool value |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-msf] (Parameter 1) |
File containing a sequence alignment | Readable sequences | Required |
-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 | EMBOSS_GRAPHICS value, or x11 |
Optional qualifiers | Allowed values | Default | |
-residuesperline | The number of residues to be displayed on each line | Any integer value | 50 |
-resbreak | Residues before a space | Integer 1 or more | Same as -residuesperline to give no breaks |
-[no]ccolours | Colour residues by their consensus value. | Yes/No | Yes |
-cidentity | Colour to display identical residues (RED) | Any string is accepted | RED |
-csimilarity | Colour to display similar residues (GREEN) | Any string is accepted | GREEN |
-cother | Colour to display other residues (BLACK) | Any string is accepted | BLACK |
-docolour | Colour residues by table oily, amide etc. | Yes/No | No |
-[no]title | Do not display the title | Yes/No | Yes |
-shade | Set to BPLW for normal shading so for pair = 1.5,1.0,0.5 and shade = BPLW Residues score Colour 1.5 or over....... BLACK (B) 1.0 to 1.5 ....... BROWN (P) 0.5 to 1.0 ....... WHEAT (L) under 0.5 ....... WHITE (W) The only four letters allowed are BPLW, in any order. | Any string is accepted | An empty string is accepted |
-pair | Values to represent identical similar related | Any string is accepted | 1.5,1.0,0.5 |
-identity | Only match those which are identical in all sequences. | Integer 0 or more | 0 |
-[no]box | Display prettyboxes | Yes/No | Yes |
-boxcol | Colour the background in the boxes | Yes/No | No |
-boxcolval | Colour to be used for background. (GREY) | Any string is accepted | GREY |
-consensus | Display the consensus | Yes/No | No |
-[no]name | Display the sequence names | Yes/No | Yes |
-maxnamelen | Margin size for the sequence name. | Any integer value | 10 |
-[no]number | Display the residue number | Yes/No | Yes |
-[no]listoptions | Display the date and options used | Yes/No | Yes |
-plurality | Plurality check value (totweight/2) | Any integer value | Half the total sequence weighting |
-[no]collision | Allow collisions in calculating consensus | Yes/No | Yes |
-alternative | Use alternative collisions routine 0) Normal collision check. (default) 1) checks identical scores with the max score found. So if any other residue matches the identical score then a collision has occurred. 2) If another residue has a greater than or equal to matching score and these do not match then a collision has occurred. 3) Checks all those not in the current consensus.If any of these give a top score for matching or identical scores then a collision has occured. | Integer from 0 to 3 | 0 |
-portrait | Set page to Portrait | Yes/No | No |
-matrixfile | Matrix file | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAMAT for DNA |
-showscore | Print residue scores | Any integer value | -1 |
Advanced qualifiers | Allowed values | Default | |
-data | (no help text) bool value | Yes/No | No |
For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAMAT is used.
EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.
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:
It exits with status 0 unless an error is reported.
Portrait mode does not cover the whole page! This is a "feature" in plplot.
Program name | Description |
---|---|
plotcon | Plots the quality of conservation of a sequence alignment |
Many features were first implemented in the EGCG program "prettyplot" by Peter Rice.
The original suggestions for the PrettyPlot program were from Denis Duboule and Sigfried Labeit at EMBL. Gert Vriend added the star marking. Rita Grandori suggested the -NOCOLLISION option.
Completed 5th May 1999.