EMBOSS: prettyplot

| ## EMBOSS: prettyplot

# Program prettyplot

## Function

Displays aligned sequences, with colouring and boxing

## Description

prettyplot reads in a set of aligned DNA or protein sequences. It displays them graphically, with conserved regions highlighted in various ways.

## Usage

Here is a sample session with 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

## Command line arguments

       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

## Input file format

Any sequence USA.

## Output file format

An image of the alignment is displayed.

## Data files

Prettyplot uses a comparison matrix file to calculate similarity to the consensus.

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:

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

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

None.

## Exit status

It exits with status 0 unless an error is reported.

## Known bugs

Portrait mode does not cover the whole page! This is a "feature" in plplot.

## See also

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

## Author(s)

This application was written by Ian Longden (il@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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.

## History

Completed 5th May 1999.

## Target users

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

## Comments