POLYDOT : Displays all-against-all dotplots of a set of sequences (EMBOSS)

your e-mail
(

= required,

= conditionally required)

input Section

required Section

output Section

Gap (in residues) between dotplots (-gap)
Draw a box around each dotplot (-boxit)
Dump all matches as feature files (-dumpfeat)
format to Dump out as (-format)
Extension for feature file (-ext)

input Section

Sequences file to be read in (-sequences) : please enter either :

the name of a file:
or the actual data here:

(sequence format)

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required Section

Word size (-wordsize)

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output Section

data Section

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data Section

Display as data (-data)

graph [device to be displayed on] (-graph)
outfile (-outfile)

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Some explanations about the options

Main parameters
Gap (in residues) between dotplots (-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.
input Section
Sequences file to be read in (-sequences): File containing a sequence alignment
enter either the name of a file or the actual data: if you are using Netscape 2.x or later, you can select a file by typing its name, or better, by selecting it with the Netscape file browser (Browse button); OR you can type your data in the next area, or cut and paste it from another application.; (but not both)

data Section
Display as data (-data): Output the match data to a file instead of plotting it
Sequence format: The sequence will be automatically converted in the format needed for the program; providing you enter a sequence either:; in plain (raw) sequence format or in one of the following known formats:; IG,GenBank,NBRF,EMBL,GCG,DNAStrider,Fitch,fasta,Phylip,PIR,MSF,ASN,PAUP,CLUSTALW; You may enter in the text area a database entry code, or an accession number, in this form:
database:entry_name
or:
database:accession.

Pise form generator version: 5.a (16 Dec 2002 11:54)