EMBOSS: prettyplot

| prettyplot

## 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 -resbreak=10 -boxcol -consensus -plurality=3
    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 -plurality=3 -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

       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,
                                      tekt, tek, none, data, xterm, png, gif)

       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)
       -resbreak           integer    [Same as -residuesperline to give no breaks]
                                      Residues before a space (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 is accepted)
       -csimilarity        string     [GREEN] Colour to display similar residues
                                      (GREEN) (Any string is accepted)
       -cother             string     [BLACK] Colour to display other residues
                                      (BLACK) (Any string is accepted)
       -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]box            boolean    [Y] Display prettyboxes
       -boxcol             boolean    [N] Colour the background in the boxes
       -boxcolval          string     [GREY] Colour to be used for background.
                                      (GREY) (Any string is accepted)
       -[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
       -plurality          float      [Half the total sequence weighting]
                                      Plurality check value (totweight/2) (Any
                                      numeric value)
       -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
       -sformat1           string     Input sequence format
       -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. 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

Standard (Mandatory) qualifiers | Allowed values | Default
--- | --- | ---
[-sequences] (Parameter 1) | (Aligned) sequence set filename and optional format, or reference (input USA) | Readable set of sequences | Required
-graph | Graph type | EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tekt, tek, none, data, xterm, png, gif | EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers | Allowed values | Default
-matrixfile | 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. | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA
-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. | Boolean 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. | Boolean value Yes/No | No
-shade | 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})?$/ | An empty string is accepted
-pair | Values to represent identical similar related | List of floating point numbers | 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 | Boolean value Yes/No | Yes
-boxcol | Colour the background in the boxes | Boolean value Yes/No | No
-boxcolval | Colour to be used for background. (GREY) | Any string is accepted | GREY
-[no]name | Display the sequence names | Boolean value Yes/No | Yes
-maxnamelen | Margin size for the sequence name. | Any integer value | 10
-[no]number | Display the residue number | Boolean value Yes/No | Yes
-[no]listoptions | Display the date and options used | Boolean value Yes/No | Yes
-plurality | Plurality check value (totweight/2) | Any numeric value | Half the total sequence weighting
-consensus | Display the consensus | Boolean value Yes/No | No
-[no]collision | Allow collisions in calculating consensus | Boolean value Yes/No | Yes
-alternative | 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. |
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.)
| 0
-showscore | Print residue scores | Any integer value | -1
-portrait | Set page to Portrait | Boolean value Yes/No | No
Advanced (Unprompted) qualifiers | Allowed values | Default
(none)

## Input file format

prettyplot reads any sequence USA.

### 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

An image of the alignment is displayed on the specified graphics device.

### Output files for usage example

### Graphics File: prettyplot.ps

### Output files for usage example 2

### Graphics File: prettyplot.ps

## 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 | Draws circular maps of DNA constructs
edialign | Local multiple alignment of sequences
emma | Multiple sequence alignment (ClustalW wrapper)
infoalign | Display basic information about a multiple sequence alignment
lindna | Draws linear maps of DNA constructs
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
prettyseq | Write a nucleotide sequence and its translation to file
remap | Display restriction enzyme binding sites in a nucleotide sequence
seealso | Finds programs with similar function to a specified program
showalign | Display a multiple sequence alignment in pretty format
showdb | Displays information on configured databases
showfeat | Display features of a sequence in pretty format
showseq | Displays sequences with features in pretty format
sixpack | Display a DNA sequence with 6-frame translation and ORFs
textsearch | Search the textual description of sequence(s)
tranalign | Generate an aligment of nucleic coding regions from aligned proteins

## Author(s)

Ian Longden (il © sanger.ac.uk)
Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

Many features were first implemented in the EGCG program "prettyplot" by Peter Rice (pmr © ebi.ac.uk)
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

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