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EMBOSS: prettyplot |
% prettyplot -resbreak=10 -boxcol -consensus -plurality=3 Displays aligned sequences, with colouring and boxing Input sequence set: globin.msf Graph type [x11]:click here for result
$ prettyplot globin.msf -plurality=3 -docolour Displays aligned sequences, with colouring and boxing Graph type [x11]:click 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) -[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) -consensus bool Display the consensus -[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. -matrixfile matrix Matrix file -showscore integer Print residue scores -portrait bool Set page to Portrait Advanced qualifiers: -data bool (no help text) bool value 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 |
-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 |
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 |
-[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 |
-consensus | Display the consensus | Yes/No | No |
-[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 |
-matrixfile | Matrix file | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA |
-showscore | Print residue scores | Any integer value | -1 |
-portrait | Set page to Portrait | Yes/No | No |
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, EDNAFULL 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:
Program name | Description |
---|---|
abiview | Reads ABI file and display the trace |
cirdna | Draws circular maps of DNA constructs |
emma | Multiple alignment program - interface to ClustalW program |
infoalign | Information on a multiple sequence alignment |
lindna | Draws linear maps of DNA constructs |
pepnet | Displays proteins as a helical net |
pepwheel | Shows protein sequences as helices |
plotcon | Plots the quality of conservation of a sequence alignment |
prettyseq | Output sequence with translated ranges |
remap | Display a sequence with restriction cut sites, translation etc |
seealso | Finds programs sharing group names |
showalign | Displays a multiple sequence alignment |
showdb | Displays information on the currently available databases |
showfeat | Show features of a sequence |
showseq | Display a sequence with features, translation etc |
textsearch | Search sequence documentation text. SRS and Entrez are faster! |
tranalign | Align nucleic coding regions given the aligned proteins |
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.