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.