This is the command tcodee that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
tcode - Identify protein-coding regions using Fickett TESTCODE statistic
SYNOPSIS
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 integer
This 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 integer
The 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 toggle
On 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
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