wordfinder1e
Match large sequences against one or more other sequences
Usage
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
Overview
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
Releases
9 releases since Debian 5.0 (Lenny); the text changed 2 times.