This is the command wordfindere 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
wordfinder - Match large sequences against one or more other sequences
SYNOPSIS
wordfinder -asequence seqset -bsequence seqall [-datafile matrixf] -gapopen float
-gapextend float [-width integer] [-wordlen integer] [-limitmatch integer]
[-limitalign integer] [-lowmatch integer] [-lowalign integer] -outfile align
[-errorfile outfile]
wordfinder -help
DESCRIPTION
wordfinder 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 seqset
-bsequence seqall
-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.
Required section
-gapopen float
Default value: @($(acdprotein)? 30.0 : 30.0)
-gapextend float
Default value: @($(acdprotein)? 1.5 : 1.5)
Additional section
-width integer
Default value: 16
-wordlen integer
Default value: 6
-limitmatch integer
-limitalign integer
-lowmatch integer
-lowalign integer
Output section
-outfile align
-errorfile outfile
Error file to be written to Default value: wordfinder.error
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