Provided by: emboss_6.6.0+dfsg-12ubuntu1_amd64
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
BUGS
Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).
SEE ALSO
wordfinder is fully documented via the tfm(1) system.
AUTHOR
Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org> Wrote the script used to autogenerate this manual page.
COPYRIGHT
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.