wordfinder(1) Match large sequences against one or more other sequences


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



is a command line program from EMBOSS ("the European Molecular Biology Open Software Suite"). It is part of the "Alignment:Local" command group(s).


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 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).


Debian Med Packaging Team <[email protected]>

Wrote the script used to autogenerate this manual page.


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.