EMBOSS: syco


Program syco

Function

Synonymous codon usage Gribskov statistic plot

Description

syco is a frame-specific gene finder that tries to recognize protein coding sequences by virtue of the similarity of their codon usage to a codon frequency table.

syco finds regions of each forward reading frame of a nucleic acid sequence that show strong codon preference. syco is useful for locating protein coding regions, determining their reading frames, estimating the level of expression of a gene, and locating nucleic acid sequencing errors.

Usage

Here is a sample session with syco, requesting graphical output.

% syco -plot -cfile pae
Synonymous codon usage Gribskov statistic plot
Input sequence: embl:paamir
Graph type [x11]: 

click here for the result with the correct codon usage file.

It is essential to use the correct codon usage file for the species. For example, click here for the result with the default codon usage file (no -cfile qualifier).

Command line arguments

   Mandatory qualifiers (* if not always prompted):
  [-sequence]          sequence   Sequence USA
*  -graph              xygraph    Graph type
*  -outfile            outfile    Output file name

   Optional qualifiers: (none)
   Advanced qualifiers:
   -cfile              codon      Codon usage file
   -window             integer    Averaging window
   -uncommon           bool       Show common codon usage
   -minimum            float      Minimum value for a common codon
   -plot               bool       Produce plot

   General qualifiers:
  -help                bool       report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose


Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence USA Readable sequence Required
-graph Graph type EMBOSS has a list of known devices, including postscript, ps, hpgl, hp7470, hp7580, meta, colourps, cps, xwindows, x11, tektronics, tekt, tek4107t, tek, none, null, text, data, xterm, png EMBOSS_GRAPHICS value, or x11
-outfile Output file name Output file <sequence>.syco
Optional qualifiers Allowed values Default
(none)
Advanced qualifiers Allowed values Default
-cfile Codon usage file Codon usage file in EMBOSS data path Ehum.cut
-window Averaging window Any integer value 30
-uncommon Show common codon usage Yes/No No
-minimum Minimum value for a common codon Number from 0.000 to 0.990 .15
-plot Produce plot Yes/No No

Input file format

Nucleic acid sequence USA.

Output file format

Graphical display.

Data files

Codon usage table files are read in.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by the EMBOSS environment variable EMBOSS_DATA.

To see the available EMBOSS data files, run:

% embossdata -showall

To fetch one of the data files (for example 'Exxx.dat') into your current directory for you to inspect or modify, run:


% embossdata -fetch -file Exxx.dat

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

Notes

None.

References

None.

Warnings

The default codon usage table file is the human Ehum.cut - caution: this may well not be the correct species.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
caiCAI codon adaptation index
chipsCodon usage statistics
codcmpCodon usage table comparison
cuspCreate a codon usage table
wobble does the analysis of the third base.

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

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