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

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

AUTHOR

Debian Med Packaging Team <[email protected]>

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.