Module Detail Information

Type: Module
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Description:chaos creates a chaos game representation (CGR) plot for a nucleotide sequence. A CGR plot represents a nucleotide sequence as a square box with an A, G, C, or T nucleotide at each corner. The box contains dots, each one representing a dinucleotide. All overlapping dinucleotides from the start to the end of the sequence are plotted. Regions which are devoid of dots (or heavily covered with dots) indicate short sequence motifs that are unusually infrequent (or frequent). CGR plots depict base composition and sequentiality and is a unique visual representation of a sequence that complements more traditional linear representations.
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
 - 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 File
 - Graph Output File
 - Graph Output Directory
 - Output Directory
File size:28.58 KB
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