Module Detail Information

Name:Supermatcher
Type: Module
Short URL:
http://bit.ly/1B7EckR
Description:supermatcher calculates an approximate alignment between all the sequences in a first set of sequences and all those from a second stream, typically a database. The alignments are written to a standard alignment file. A combination of a word-match and Smith-Waterman local alignment (dynamic programming) algorithms are used. The alignments will be less acurate than an optimal alignment generated by full dynamic programming, but the program will run faster and use less memory, which means it is suitable for use with larger sequences.
Executable:
/supermatcher
Input Parameters:
 - A Sequence
 - B Sequence
 - A Start
 - A End
 - A Reverse
 - A Ask
 - A Nucleotide
 - A Protein
 - A Lower Case
 - A Upper Case
 - A Format
 - A Database Name
 - A Entry Name
 - A UFO Features
 - A Features Format
 - A Features File
 - Gap Opening Penalty
 - Gap Extension Penalty
 - B Start
 - B End
 - B Reverse
 - B Ask
 - B Nucleotide
 - B Protein
 - B Lower Case
 - B Upper Case
 - B Format
 - B Database Name
 - B Entry Name
 - B UFO Features
 - B Features Format
 - B Features File
 - Alignment format
 - File Name extension
 - Base file name
 - Alignment width
 - Show Accession Number
 - Show Description
 - Show Full USA
 - Show Full sequence
 - Turn Off Prompts
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Data File
 - Minimum Alignment Score
 - Alignment Width
 - Word Length
Output Parameters:
 - Output
 - Output directory
 - Error File
 - Error File Directory
File size:35.45 KB
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