                                   polydot



Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Draw dotplots for all-against-all comparison of a sequence set

Description

   polydot generates a dotplot for each of an all-against-all comparison
   of a set of sequences. The dotplots are rendered on a single diagram.
   The dotplot is an intuitive graphical representation of the regions of
   similarity between two sequences. All positions from the first input
   sequence are compared with all positions from the second input sequence
   searching for exact matches between sequence regions ("words"). The two
   sequences are the axes of the rectangular dotplot. Wherever there is
   "similarity" between a word from each sequences a dot is plotted. The
   wordsize is specified by the user. Optionally, information on the
   sequence and location of all the exact matching regions may be written
   to file as a feature file.

Algorithm

   All sequence words of the specified size from the first input sequence
   are compared with all words from the second input sequence and exact
   matches identified. A line is plotted on the dotplot corresponding to
   any exact matching words. Thus any local regions of identity correspond
   to diagonals in the dotplot.

Usage

   Here is a sample session with polydot


% polydot globins.fasta -gtitle="Polydot of globins.fasta" -graph cps
Draw dotplots for all-against-all comparison of a sequence set
Word size [6]:

Created polydot.ps


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

Command line arguments

Draw dotplots for all-against-all comparison of a sequence set
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequences]         seqset     File containing a sequence alignment
   -wordsize           integer    [6] Word size (Integer 2 or more)
*  -outfeat            featout    [unknown.gff] Output features UFO
   -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:
   -[no]boxit          boolean    [Y] Draw a box around each dotplot
   -dumpfeat           toggle     [N] Dump all matches as feature files

   Advanced (Unprompted) qualifiers:
   -gap                integer    [10] This specifies the size of the gap that
                                  is used to separate the individual dotplots
                                  in the display. The size is measured in
                                  residues, as displayed in the output.
                                  (Integer 0 or more)

   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

   "-outfeat" associated qualifiers
   -offormat           string     Output feature format
   -ofopenfile         string     Features file name
   -ofextension        string     File name extension
   -ofdirectory        string     Output directory
   -ofname             string     Base file name
   -ofsingle           boolean    Separate file for each entry

   "-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

   polydot reads in a set of nucleic or protein sequences.

   The sequences may or may not be aligned.

  Input files for usage example

  File: globins.fasta

>HBB_HUMAN Sw:Hbb_Human => HBB_HUMAN
VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKV
KAHGKKVLGAFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGK
EFTPPVQAAYQKVVAGVANALAHKYH
>HBB_HORSE Sw:Hbb_Horse => HBB_HORSE
VQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKV
KAHGKKVLHSFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGK
DFTPELQASYQKVVAGVANALAHKYH
>HBA_HUMAN Sw:Hba_Human => HBA_HUMAN
VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGK
KVADALTNAVAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPA
VHASLDKFLASVSTVLTSKYR
>HBA_HORSE Sw:Hba_Horse => HBA_HORSE
VLSAADKTNVKAAWSKVGGHAGEYGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGK
KVGDALTLAVGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPA
VHASLDKFLSSVSTVLTSKYR
>MYG_PHYCA Sw:Myg_Phyca => MYG_PHYCA
VLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRFKHLKTEAEMKASED
LKKHGVTVLTALGAILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHP
GDFGADAQGAMNKALELFRKDIAAKYKELGYQG
>GLB5_PETMA Sw:Glb5_Petma => GLB5_PETMA
PIVDTGSVAPLSAAEKTKIRSAWAPVYSTYETSGVDILVKFFTSTPAAQEFFPKFKGLTT
ADQLKKSADVRWHAERIINAVNDAVASMDDTEKMSMKLRDLSGKHAKSFQVDPQYFKVLA
AVIADTVAAGDAGFEKLMSMICILLRSAY
>LGB2_LUPLU Sw:Lgb2_Luplu => LGB2_LUPLU
GALTESQAALVKSSWEEFNANIPKHTHRFFILVLEIAPAAKDLFSFLKGTSEVPQNNPEL
QAHAGKVFKLVYEAAIQLQVTGVVVTDATLKNLGSVHVSKGVADAHFPVVKEAILKTIKE
VVGAKWSEELNSAWTIAYDELAIVIKKEMNDAA

Output file format

   A graphical image is displayed on the specified graphics device.

  Output files for usage example

  Graphics File: polydot.ps

   [polydot results]

Data files

   None.

Notes

   Where the two sequences have substantial regions of identity, longer
   diagonal lines appear in the plot. It is possible to see at a glance
   such local regions of identity. It is also easy to see other features
   such as repeats (which form parallel diagonal lines), and insertions or
   deletions (which form breaks or discontinuities in the diagonal lines).

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   0 if successful.

Known bugs

   None.

See also

                    Program name                        Description
                    dotmatcher   Draw a threshold dotplot of two sequences
                    dotpath      Draw a non-overlapping wordmatch dotplot of two sequences
                    dottup       Display a wordmatch dotplot of two sequences

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.

History

                    Completed 2nd June 1999.

Target users

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

Comments

                    None
