CPGPLOT : Plot CpG rich areas (EMBOSS)

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(

= required,

= conditionally required)

input Section

required Section

output Section

input Section

sequence -- DNA [sequences] (-sequence) : please enter either :

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

(sequence format)

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required Section

Window size (-window)

Window shift increment (-shift)

Minimum length of an island (-minlen)

Minimum observed/expected (-minoe)

Minimum percentage (-minpc)

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output Section

outfile (-outfile)

graph (-graph)
Show observed/expected threshold line (-obsexp)
Show CpG rich regions (-cg)
Show percentage line (-pc)

feature file for output (-featout)

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Some explanations about the options

input Section
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)
required Section
Window size (-window): The percentage CG content and the Observed frequency of CG is calculated within a window whose size is set by this parameter. The window is moved down the sequence and these statistics are calculated at each postition that the window is moved to.
Window shift increment (-shift): This determines the number of bases that the window is moved each time after values of the percentage CG content and the Observed frequency of CG are calculated within the window.
Minimum length of an island (-minlen): This sets the minimum length that a CpG island has to be before it is reported.
Minimum observed/expected (-minoe): This sets the minimum average observed to expected ratio of C plus G to CpG in a set of 10 windows that are required before a CpG island is reported.
Minimum percentage (-minpc): This sets the minimum average percentage of G plus C a set of 10 windows that are required before a CpG island is reported.
output Section
outfile (-outfile): This sets the name of the file holding the report of the input sequence name, CpG island parameters and the output details of any CpG islands that are found.
Show observed/expected threshold line (-obsexp): If this is set to true then the graph of the observed to expected ratio of C plus G to CpG within a window is displayed.
Show CpG rich regions (-cg): If this is set to true then the graph of the regions which have been determined to be CpG islands is displayed.
Show percentage line (-pc): If this is set to true then the graph of the percentage C plus G within a window is displayed.
feature file for output (-featout): File for output features
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 11:53)