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EMBOSS: syco |
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.
% 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).
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 |
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 | 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 |
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:
Program name | Description |
---|---|
chips | Codon usage statistics |
cusp | Create a codon usage table |
getorf | Finds and extracts open reading frames (ORFs) |