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polydot |
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.
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.
% 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
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,
tekt, tek, none, data, xterm, png, gif)
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. 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
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| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequences] (Parameter 1) |
File containing a sequence alignment | Readable set of sequences | Required |
| -wordsize | Word size | Integer 2 or more | 6 |
| -outfeat | Output features UFO | Writeable feature table | unknown.gff |
| -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 | |
| -[no]boxit | Draw a box around each dotplot | Boolean value Yes/No | Yes |
| -dumpfeat | Dump all matches as feature files | Toggle value Yes/No | No |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -gap | 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 |
The sequences may or may not be aligned.
>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 |
![[polydot results]](polydot.1.polydot.gif)
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).
| 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 |