This is the command supermatchere that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
supermatcher - Calculate approximate local pair-wise alignments of larger sequences
SYNOPSIS
supermatcher -asequence seqall -bsequence seqset [-datafile matrixf] [-minscore float]
-gapopen float -gapextend float [-width integer] [-wordlen integer]
-outfile align [-errorfile outfile]
supermatcher -help
DESCRIPTION
supermatcher is a command line program from EMBOSS (“the European Molecular Biology Open
Software Suite”). It is part of the "Alignment:Local" command group(s).
OPTIONS
Input section
-asequence seqall
-bsequence seqset
-datafile matrixf
This is the scoring matrix file used when comparing sequences. By default it is the
file 'EBLOSUM62' (for proteins) or the file 'EDNAFULL' (for nucleic sequences). These
files are found in the 'data' directory of the EMBOSS installation.
-minscore float
Minimum alignment score to report an alignment.
Required section
-gapopen float
Default value: @($(acdprotein)? 10.0 : 10.0)
-gapextend float
Default value: @($(acdprotein)? 0.5 : 0.5)
Additional section
-width integer
Default value: 16
-wordlen integer
Default value: 6
Output section
-outfile align
-errorfile outfile
Error file to be written to for failed alignments Default value: supermatcher.error
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