cpgplot1e
Identify and plot cpg islands in nucleotide sequence(s)
Usage
cpgplot -sequence
seqall
-window
integer
-minlen
integer
-minoe
float
-minpc
float
-outfile
outfile
-plot
toggle
-graph
xygraph
-obsexp
boolean
-cg
boolean
-pc
boolean
-outfeat
featout
cpgplot -help
Overview
cpgplot is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Nucleic:CpG Islands" command group(s).
Options
Input section
-
-sequence seqall
Required section
-
-window integer -
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 position that the window is moved to. Default value: 100
-
-minlen integer -
This sets the minimum length that a CpG island has to be before it is reported. Default value: 200
-
-minoe float -
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. Default value: 0.6
-
-minpc float -
This sets the minimum average percentage of G plus C a set of 10 windows that are required before a CpG island is reported. Default value: 50.
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.
-
-plot toggle -
Default value: Y
-
-graph xygraph
-
-obsexp boolean -
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. Default value: Y
-
-cg boolean -
If this is set to true then the graph of the regions which have been determined to be CpG islands is displayed. Default value: Y
-
-pc boolean -
If this is set to true then the graph of the percentage C plus G within a window is displayed. Default value: Y
-
-outfeat featout -
File for output features
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.