EMBOSS: prettyplot


Program prettyplot

Displays aligned sequences, with colouring and boxing

Function

Displays aligned sequences, with colouring and boxing

Description

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

Usage

Here is a sample session with prettyplot.
% prettyplot $EMBOSS_DATA/globin.msf -resbreak=10 -boxcol -consensus -plurality=3
click here for result
$ prettyplot $EMBOSS_DATA/globin.msf -plurality=3 -docolour
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)
   -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

Input file format

Any sequence USA.

Output file format

.ps file if postscipt output requested.

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, 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:

Notes

References

Warnings

Diagnostic Error Messages

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 nameDescription
plotconPlots the quality of conservation of a sequence alignment

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