Module Detail Information

Name:Syco
Type: Module
Short URL:
http://bit.ly/1B7Efgq
Description: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. Optionally the most common codon usage can be displayed, based on a minimum fraction of the codons for an amino acid.
Executable:
/syco
Input Parameters:
 - Sequence
 - Start
 - End
 - Reverse
 - Ask
 - Nucleotide
 - Protein
 - Lower Case
 - Upper Case
 - Format
 - Database Name
 - Entry Name
 - UFO Features
 - Features Format
 - Features File
 - Turn Off Prompts
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Codon Usage File
 - Codon Usage File Format
 - Graph Type
 - Graph Prompting
 - Graph Description
 - Graph Title
 - Graph Subtitle
 - Graph X-Axis Title
 - Graph Y-Axis Title
 - Averaging Window
 - Show Common Codon Usage
 - Minimum Value for Common Codon
 - Plot
 - Version
Output Parameters:
 - Output Syco File
 - Graph Output File
 - Graph Output Directory
 - Output Directory
File size:29.88 KB
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