syco

Function

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.

It is essential to use the correct codon usage file for the species.

Usage

Command line arguments


Input file format

syco reads a nucleic acid sequence USA.

Output file format

Data files

Codon usage table files are read in.

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. wobble does the analysis of the third base.

Author(s)

History

Target users

Comments