polydot

 

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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:6.4.0.0

   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
   -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

   "-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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-sequences]
(Parameter 1)		 seqset File containing a sequence alignment Readable set of sequences Required
-wordsize integer Word size Integer 2 or more 6
-outfeat featout Output features UFO Writeable feature table unknown.gff
-graph graph Graph type EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, pdf, svg EMBOSS_GRAPHICS value, or x11
Additional (Optional) qualifiers
-[no]boxit boolean Draw a box around each dotplot Boolean value Yes/No Yes
-dumpfeat toggle Dump all matches as feature files Toggle value Yes/No No
Advanced (Unprompted) qualifiers
-gap integer 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 10
Associated qualifiers
"-sequences" associated seqset qualifiers
-sbegin1
-sbegin_sequences		 integer Start of each sequence to be used Any integer value 0
-send1
-send_sequences		 integer End of each sequence to be used Any integer value 0
-sreverse1
-sreverse_sequences		 boolean Reverse (if DNA) Boolean value Yes/No N
-sask1
-sask_sequences		 boolean Ask for begin/end/reverse Boolean value Yes/No N
-snucleotide1
-snucleotide_sequences		 boolean Sequence is nucleotide Boolean value Yes/No N
-sprotein1
-sprotein_sequences		 boolean Sequence is protein Boolean value Yes/No N
-slower1
-slower_sequences		 boolean Make lower case Boolean value Yes/No N
-supper1
-supper_sequences		 boolean Make upper case Boolean value Yes/No N
-sformat1
-sformat_sequences		 string Input sequence format Any string  
-sdbname1
-sdbname_sequences		 string Database name Any string  
-sid1
-sid_sequences		 string Entryname Any string  
-ufo1
-ufo_sequences		 string UFO features Any string  
-fformat1
-fformat_sequences		 string Features format Any string  
-fopenfile1
-fopenfile_sequences		 string Features file name Any string  
"-outfeat" associated featout qualifiers
-offormat string Output feature format Any string  
-ofopenfile string Features file name Any string  
-ofextension string File name extension Any string  
-ofdirectory string Output directory Any string  
-ofname string Base file name Any string  
-ofsingle boolean Separate file for each entry Boolean value Yes/No N
"-graph" associated graph qualifiers
-gprompt boolean Graph prompting Boolean value Yes/No N
-gdesc string Graph description Any string Poly dotplot
-gtitle string Graph title Any string  
-gsubtitle string Graph subtitle Any string  
-gxtitle string Graph x axis title Any string  
-gytitle string Graph y axis title Any string  
-goutfile string Output file for non interactive displays Any string  
-gdirectory string Output directory Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 Displays 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 © 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