Module Detail Information

Type: Module
Short URL:
Description:einverted finds inverted repeats (stem loops) in nucleotide sequences. It identifies regions of local alignment of the input sequence and its reverse complement that exceed a threshold score. The alignments may include a proportion of mismatches and gaps, which correspond to bulges in the stem loop. One or more sequences are read and a file with the sequence(s) (without gap characters) of the inverted repeat regions is written. It can find multiple inverted repeats in a sequence. Only non-overlapping matches are reported.
Input Parameters:
 - Sequence
 - Start
 - End
 - Reverse
 - Ask
 - Nucleotide
 - Protein
 - Lower Case
 - Upper Case
 - Format
 - Database Name
 - Entry Name
 - UFO Features
 - Features Format
 - Features File
 - Output Sequence Format
 - Output Sequence Extension
 - Output Sequence Directory
 - Output Sequence Base file name
 - Turn Off Prompts
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Database Name to Add
 - Output Sequence Seperate Files
 - Output Sequence UFO Features
 - Output Sequence Features Format
 - Output Sequence Features File Name
 - Output Sequence Features Output Directory
 - Gap Penalty
 - Minimum Score Threshold
 - Match Score
 - Mismatch Score
 - Output Directory
 - Maximum Repeat
Output Parameters:
 - Output Sequence
 - Output
File size:30.15 KB
View Source    Download    Open