| plotcon

## Function

Plots the quality of conservation of a sequence alignment

## Description

Displays a graphical representation of the similarity along a set of aligned sequences.

The similarity is calculated by moving a window of a specified length along the aligned sequences. Within the window, the similarity of any one position is taken to be the average of all the possible pairwise scores of the bases or residues at that position. The pairwise scores are taken from the specified similarity matrix. The average of the position similarities within the window is plotted.

The program is useful for determining where the quality of alignments is good or bad.

The average similarity is calculated by:

    Av. Sim. =       sum( Mij*wi + Mji*w2  )
                          -------------------
                      (Nseq*Wsize)*((Nseq-1)*Wsize)

sum - over column*window size
w - sequence weighting
M - matrix comparison table
i,j - with respect to residue i or j
Nseq - number of sequences in the alignment
Wsize - window size

## Usage

Here is a sample session with plotcon

    % plotcon -sformat msf ../../data/globins.msf -graph cps
    Plots the quality of conservation of a sequence alignment
    Window size [4]:

    Created plotcon.ps

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

## Command line arguments

       Mandatory qualifiers (* if not always prompted):
      [-msf]               seqset     File containing a sequence alignment
       -winsize            integer    Number of columns to average alignment
                                      quality over. The larger this value is, the
                                      smoother the plot will be.
    *  -graph              xygraph    Graph type
    *  -outfile            outfile    Display as data

       Optional qualifiers:
       -scorefile          matrix     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.

       Advanced qualifiers:
       -data               boolean    Output the match data to a file instead of
                                      plotting it

       Associated qualifiers:
      "-msf" related qualifiers
       -sbegin1             integer    First base used
       -send1               integer    Last base used, def=seq length
       -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
       -sopenfile1          string     Input filename
       -sdbname1            string     Database name
       -sid1                string     Entryname
       -ufo1                string     UFO features
       -fformat1            string     Features format
       -fopenfile1          string     Features file name
      "-graph" related qualifiers
       -gprompt             boolean    Graph prompting
       -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
      "-outfile" related qualifiers
       -odirectory          string     Output directory

       General qualifiers:
       -auto                boolean    Turn off prompts
       -stdout              boolean    Write standard output
       -filter              boolean    Read standard input, write standard output
       -options             boolean    Prompt for required and optional values
       -debug               boolean    Write debug output to program.dbg
       -acdlog              boolean    Write ACD processing log to program.acdlog
       -acdpretty           boolean    Rewrite ACD file as program.acdpretty
       -acdtable            boolean    Write HTML table of options
       -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 deaths

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-msf] (Parameter 1) | File containing a sequence alignment | Readable sequences | Required
-winsize | Number of columns to average alignment quality over. The larger this value is, the smoother the plot will be. | Any integer value | 4
-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
-outfile | Display as data | Output file | <sequence>.plotcon
Optional qualifiers | Allowed values | Default
-scorefile | 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
Advanced qualifiers | Allowed values | Default
-data | Output the match data to a file instead of plotting it | Boolean value Yes/No | No

## Input file format

plotcon reads a set of gapped, aligned sequences.

### Input files for usage example

### File: ../../data/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: 0.14
      Name: HBB_HORSE Len: 164  Check: 6007 Weight: 0.15
      Name: HBA_HUMAN Len: 164  Check: 3921 Weight: 0.15
      Name: HBA_HORSE Len: 164  Check: 4770 Weight: 0.19
      Name: MYG_PHYCA Len: 164  Check: 7930 Weight: 0.23
      Name: GLB5_PETMA Len: 164  Check: 1857 Weight: 0.21
      Name: LGB2_LUPLU Len: 164  Check: 2879 Weight: 0.10

    //

               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

A graph of the quality of the alignment is dispalyed on the specifed graphics device.

### Output files for usage example

### Graphics File: plotcon.ps

## Data files

It reads in the specified similarity matrix.

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

None.

## References

None.

## Warnings

If you give it a set of unaligned sequences, it will plot the (poor!) quality of these as if they were aligned.

## Diagnostic Error Messages

None.

## Exit status

It always exits with status 0.

## Known bugs

None.

## See also

Program name | Description
--- | ---
emma | Multiple alignment program - interface to ClustalW program
infoalign | Information on a multiple sequence alignment
prettyplot | Displays aligned sequences, with colouring and boxing
showalign | Displays a multiple sequence alignment
tranalign | Align nucleic coding regions given the aligned proteins

## Author(s)

Tim Carver (tcarver © hgmp.mrc.ac.uk)
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

## History

Written (Sept 2000) - Tim Carver.

## Target users

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

## Comments