TCODE(1e) | EMBOSS Manual for Debian | TCODE(1e) |
NAME¶
tcode - Identify protein-coding regions using Fickett TESTCODE statisticSYNOPSIS¶
tcode -sequence seqall -datafile datafile -window integer -step integer -plot toggle -outfile report -graph xygraph
tcode -help
DESCRIPTION¶
tcode is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Nucleic:Gene finding" command group(s).OPTIONS¶
Input section¶
-sequence seqall-datafile datafile
The default data file is Etcode.dat and contains coding
probabilities for each base. The probabilities are for both positional and
compositional information. Default value: Etcode.dat
Required section¶
-window integerThis is the number of nucleotide bases over which the
TESTCODE statistic will be performed each time. The window will then slide
along the sequence, covering the same number of bases each time. Default
value: 200
Advanced section¶
-step integerThe selected window will, by default, slide along the
nucleotide sequence by three bases at a time, retaining the frame (although
the algorithm is not frame sensitive). This may be altered to increase or
decrease the increment of the slide. Default value: 3
Output section¶
-plot toggleOn selection a graph of the sequence (X axis) plotted
against the coding score (Y axis) will be displayed. Sequence above the green
line is coding, that below the red line is non-coding. Default value: N
-outfile report
-graph xygraph
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¶
tcode 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 |