CPGPLOT(1e) | EMBOSS Manual for Debian | CPGPLOT(1e) |
NAME¶
cpgplot - Identify and plot CpG islands in nucleotide sequence(s)SYNOPSIS¶
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
DESCRIPTION¶
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 seqallRequired section¶
-window integerThe 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 outfileThis 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
BUGS¶
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).SEE ALSO¶
cpgplot is fully documented via the tfm(1) system.AUTHOR¶
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>Wrote the script used to autogenerate this manual
page.
COPYRIGHT¶
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.
05/11/2012 | EMBOSS 6.4.0 |