syco may 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. Given a codon usage file and an input nucleotide sequence, syco draws a plot of the synonymous codon usage Gribskov statistic calculated for windows over the sequence. The same data may be written to an output file. 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.
|
|
The default codon usage table file is the human Ehum.cut - caution: this may well not be the correct species.