Module Detail Information

Name:CpG Report
Type: Module
Short URL:
http://bit.ly/1B7EdoI
Description:cpgreport identifies in a nucleotide sequence regions with higher than expected frequency of the dinucleotide CG. Each position in the sequence is scored using a running sum calculated from all positions in the sequence. This is a different method to that typically used for identifying CpG islands, for example by newcpgreport and cpgplot. This method overpredicts islands but finds the smaller ones around primary exons. An output file is written with information on the CpG-rich regions that are found. A feature table of sequence features in these regions is also written.
Executable:
/cpgreport
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
 - Version
 - CG Score
 - Output Features Format
 - Features Filename
 - Features Extension
 - Features Base Filename
 - Features Seperate Files
Output Parameters:
 - Output File
 - Output Directory
 - Output Features File
 - Features Directory
File size:26.23 KB
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