Module Detail Information

Name:Etandem
Type: Module
Short URL:
http://bit.ly/1B7EfNp
Description:etandem identifies tandem repeats in a nucleotide sequence. It calculates a consensus sequence for a putative repeat region and scores potential repeats based on the number of matches and mismatches there are to the consensus. For a repeat to be identified, it must be within the specified minimum and maximum size and must score higher than the specified threshold score. The output is a standard EMBOSS report file with details of the location and score of any tandem repeats. Optionally, the output can be written in the format of the Sanger Centre quicktandem program. Running etandem with a wide range of repeat sizes is inefficient. It is normally used after equicktandem has been run to identify putative sizes and locations of repeats.
Executable:
/etandem
Input Parameters:
 - Sequence
 - Start
 - End
 - Reverse
 - Ask
 - Nucleotide
 - Protein
 - Lower Case
 - Upper Case
 - Format
 - Database Name
 - Entry Name
 - UFO Features
 - Features Format
 - Features File
 - Report Format
 - Report Extension
 - Report Directory
 - Report Base file name
 - Turn Off Prompts
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Minimum Score Threshold
 - Mismatch Score
 - Maximum Repeat
 - Minimum Repeat Size
 - Maximum Repeat Size
 - Allow Uniform Consensus
 - Show Accession number in Report
 - Show Description in Report
 - Show Score in Report
 - Show Full USA
 - Maximum Total Hits
 - Maximum Hits for One Sequence
Output Parameters:
 - Output Report File
 - Output Orig File
 - Orig Output Directory
File size:30.17 KB
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