Module Detail Information

Name:Matcher
Type: Module
Short URL:
http://bit.ly/1B7EcBb
Description:matcher compares two sequences looking for local sequence similarities using a rigorous algorithm. matcher is based on Bill Pearson's 'lalign' application, version 2.0u4 Feb. 1996 Lalign uses code developed by X. Huang and W. Miller (Adv. Appl. Math. (1991) 12:337-357) for the "sim" program, which is a linear-space version of an algorithm described by M. S. Waterman and M. Eggert (J. Mol. Biol. 197:723-728). Like water, matcher is rigorous, but also very slow. The advantage of matcher is that it uses far less memory than water, so you are much less likely to run out of memory when aligning large sequences. matcher will also report a specified number of alignments between the two sequences showing the actual local alignments. (water will only report the single best match.) The default number of alignments output is 1, but can be increased to (for example) the 10 best alignments by using the '-alternatives 10' command-line qualifier. In some cases, for example multidomain proteins or cDNA and genomic DNA comparisons, there may be many interesting and significant alignments.
Executable:
/matcher
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
 - Scoring Matrix file
 - Alternatives
 - 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
 - Output directory
 - 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
Output Parameters:
 - Output
File size:35.04 KB
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