                                 prettyplot



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Function

   Draw a sequence alignment with pretty formatting

Description

   prettyplot draws a plot of the input sequence alignment. The sequences
   are rendered in pretty formatting on the specified graphics device.
   Drawing options control the appearance of the image, such as boxes,
   colour and shading for highlighting conserved regions.

Usage

   Here is a sample session with prettyplot


% prettyplot -blocksperline=5 -boxcol -consensus -ratio=0.59
Draw a sequence alignment with pretty formatting
Input (aligned) sequence set: globins.msf
Graph type [x11]: cps

Created prettyplot.ps


   Go to the input files for this example
   Go to the output files for this example

   Example 2


% prettyplot globins.msf -ratio=0.59 -docolour
Draw a sequence alignment with pretty formatting
Graph type [x11]: cps

Created prettyplot.ps


   Go to the output files for this example

Command line arguments

Draw a sequence alignment with pretty formatting
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequences]         seqset     (Aligned) sequence set filename and optional
                                  format, or reference (input USA)
   -graph              graph      [$EMBOSS_GRAPHICS value, or x11] Graph type
                                  (ps, hpgl, hp7470, hp7580, meta, cps, x11,
                                  tek, tekt, none, data, xterm, png, gif, pdf,
                                  svg)

   Additional (Optional) qualifiers:
   -matrixfile         matrix     [EBLOSUM62 for protein, EDNAFULL for DNA]
                                  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.
   -residuesperline    integer    [50] The number of residues to be displayed
                                  on each line (Any integer value)
   -blocksperline      integer    [1] Blocks of residues on each line (Integer
                                  1 or more)
   -[no]ccolours       boolean    [Y] Colour residues by their consensus
                                  value.
   -cidentity          string     [RED] Colour to display identical residues
                                  (RED) (Any string)
   -csimilarity        string     [GREEN] Colour to display similar residues
                                  (GREEN) (Any string)
   -cother             string     [BLACK] Colour to display other residues
                                  (BLACK) (Any string)
   -docolour           boolean    [N] Colour residues by table oily, amide
                                  etc.
   -shade              string     Set to BPLW for normal shading
                                  (black, pale, light, white)
                                  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 up to 4 characters,
                                  matching regular expression
                                  /^([BPLW]{4})?$/)
   -pair               array      [1.5,1.0,0.5] Values to represent identical
                                  similar related
   -identity           integer    [0] Only match those which are identical in
                                  all sequences. (Integer 0 or more)
   -[no]doboxes        boolean    [Y] Display prettyboxes
   -boxcol             boolean    [N] Colour the background in the boxes
   -boxuse             string     [GREY] Colour to be used for background.
                                  (GREY) (Any string)
   -[no]name           boolean    [Y] Display the sequence names
   -maxnamelen         integer    [10] Margin size for the sequence name. (Any
                                  integer value)
   -[no]number         boolean    [Y] Display the residue number
   -[no]listoptions    boolean    [Y] Display the date and options used
   -ratio              float      [0.5] Plurality ratio for a consensus match
                                  (Number from 0.000 to 1.000)
   -consensus          boolean    [N] Display the consensus
   -[no]collision      boolean    [Y] Allow collisions in calculating
                                  consensus
   -alternative        menu       [0] Values are 0:Normal collision check.
                                  (default)
                                  1:Compares 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. (Values: 0 (Normal
                                  collision check. (default)); 1 (Compares
                                  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.))
   -showscore          integer    [-1] Print residue scores (Any integer
                                  value)
   -portrait           boolean    [N] Set page to Portrait

   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-sequences" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -scircular1         boolean    Sequence is circular
   -squick1            boolean    Read id and sequence only
   -sformat1           string     Input sequence format
   -iquery1            string     Input query fields or ID list
   -ioffset1           integer    Input start position offset
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-graph" associated qualifiers
   -gprompt            boolean    Graph prompting
   -gdesc              string     Graph description
   -gtitle             string     Graph title
   -gsubtitle          string     Graph subtitle
   -gxtitle            string     Graph x axis title
   -gytitle            string     Graph y axis title
   -goutfile           string     Output file for non interactive displays
   -gdirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit


Input file format

   prettyplot reads aligned protein sequences.

   The input is a standard EMBOSS sequence query (also known as a 'USA').

   Major sequence database sources defined as standard in EMBOSS
   installations include srs:embl, srs:uniprot and ensembl

   Data can also be read from sequence output in any supported format
   written by an EMBOSS or third-party application.

   The input format can be specified by using the command-line qualifier
   -sformat xxx, where 'xxx' is replaced by the name of the required
   format. The available format names are: gff (gff3), gff2, embl (em),
   genbank (gb, refseq), ddbj, refseqp, pir (nbrf), swissprot (swiss, sw),
   dasgff and debug.

   See: http://emboss.sf.net/docs/themes/SequenceFormats.html for further
   information on sequence formats.

  Input files for usage example

  File: globins.msf

!!AA_MULTIPLE_ALIGNMENT 1.0

  ../data/globins.msf MSF:  164 Type: P 25/06/01 CompCheck: 4278 ..

  Name: HBB_HUMAN Len: 164  Check: 6914 Weight: 0.61
  Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.65
  Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.65
  Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.83
  Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 1.00
  Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.91
  Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.43

//

           1                                               50
HBB_HUMAN  ~~~~~~~~VHLTPEEKSAVTALWGKVN.VDEVGGEALGR.LLVVYPWTQR
HBB_HORSE  ~~~~~~~~VQLSGEEKAAVLALWDKVN.EEEVGGEALGR.LLVVYPWTQR
HBA_HUMAN  ~~~~~~~~~~~~~~VLSPADKTNVKAA.WGKVGAHAGEYGAEALERMFLS
HBA_HORSE  ~~~~~~~~~~~~~~VLSAADKTNVKAA.WSKVGGHAGEYGAEALERMFLG
MYG_PHYCA  ~~~~~~~VLSEGEWQLVLHVWAKVEAD.VAGHGQDILIR.LFKSHPETLE
GLB5_PETMA PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQE
LGB2_LUPLU ~~~~~~~~GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKD

           51                                             100
HBB_HUMAN  FFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE
HBB_HORSE  FFDSFGDLSNPGAVMGNPKVKAHGKKVLHSFGEGVHHLDNLKGTFAALSE
HBA_HUMAN  FPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD
HBA_HORSE  FPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLAVGHLDDLPGALSNLSD
MYG_PHYCA  KFDRFKHLKTEAEMKASEDLKKHGVTVLTALGAILKKKGHHEAELKPLAQ
GLB5_PETMA FFPKFKGLTTADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRD
LGB2_LUPLU LFSFLKGTSEVPQNNPELQAHAGKVFKLVYEAAIQLQVTGVVVTDATLKN

           101                                            150
HBB_HUMAN  LHCDKLH..VDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVA
HBB_HORSE  LHCDKLH..VDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVA
HBA_HUMAN  LHAHKLR..VDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVS
HBA_HORSE  LHAHKLR..VDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVS
MYG_PHYCA  SHATKHK..IPIKYLEFISEAIIHVLHSRHPGDFGADAQGAMNKALELFR
GLB5_PETMA LSGKHAK..SFQVDPQYFKVLAAVIADTVAAGDAGFEKLMSMICILLRSA
LGB2_LUPLU LGSVHVSKGVADAHFPVVKEAILKTIKEVVGAKWSEELNSAWTIAYDELA

           151        164
HBB_HUMAN  NALAHKYH~~~~~~
HBB_HORSE  NALAHKYH~~~~~~
HBA_HUMAN  TVLTSKYR~~~~~~
HBA_HORSE  TVLTSKYR~~~~~~
MYG_PHYCA  KDIAAKYKELGYQG
GLB5_PETMA Y~~~~~~~~~~~~~
LGB2_LUPLU IVIKKEMNDAA~~~


Output file format

   The output is to the specified graphics device.

   The results can be output in one of several formats by using the
   command-line qualifier -graph xxx, where 'xxx' is replaced by the name
   of the required device. Support depends on the availability of
   third-party software packages.

   The device names that output to a file are: ps (postscript), cps
   (colourps), png, gif, pdf, svg, hpgl, hp7470, hp7580, das, data.

   The other available device names are: meta, x11 (xwindows), tek
   (tek4107t), tekt (tektronix), xterm, text.

   Output can be turned off by specifying none (null).

   See: http://emboss.sf.net/docs/themes/GraphicsDevices.html for further
   information on supported devices.

  Output files for usage example

  Graphics File: prettyplot.ps

   [prettyplot results]

  Output files for usage example 2

  Graphics File: prettyplot.ps

   [prettyplot results]

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 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:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

   A consesnsus sequence is calculated for the alignment and individual
   sequences compared to the consensus using the specified comparison
   matrix file. The default matrix for protein sequences is EBLOSUM62 and
   for nucleotide sequences is EDNAFULL. The drawing options render
   conserved sites and regions identified from the comparisons. For
   example, residues in a sequence are classed as "identical", "similar"
   or "other" to the consensus depending on user-specified thresholds of
   sequence similarity (-pair option). Residues in each class are rendered
   red, green and black by default (this can be changed).

   There are other more general drawing options, for example, controlling
   the number of residues displayed per line, background shading and
   whether to display sequence names or not.

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          Display the trace in an ABI sequencer file
   cirdna           Draw circular map of DNA constructs
   edialign         Local multiple alignment of sequences
   emma             Multiple sequence alignment (ClustalW wrapper)
   iep              Calculate the isoelectric point of proteins
   infoalign        Display basic information about a multiple sequence alignment
   lindna           Draw linear maps of DNA constructs
   pepinfo          Plot amino acid properties of a protein sequence in parallel
   pepnet           Draw a helical net for a protein sequence
   pepwheel         Draw a helical wheel diagram for a protein sequence
   plotcon          Plot conservation of a sequence alignment
   plotorf          Plot potential open reading frames in a nucleotide sequence
   prettyseq        Write a nucleotide sequence and its translation to file
   remap            Display restriction enzyme binding sites in a nucleotide sequence
   showalign        Display a multiple sequence alignment in pretty format
   showfeat         Display features of a sequence in pretty format
   showpep          Display protein sequences with features in pretty format
   sixpack          Display a DNA sequence with 6-frame translation and ORFs
   tranalign        Generate an alignment of nucleic coding regions from aligned
                    proteins

Author(s)

   Ian Longden formerly at:
   Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
   CB10 1SA, UK.

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

   Many features were first implemented in the EGCG program "prettyplot"
   by Peter Rice
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

   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

   None
