man supermatcher (1): Calculate approximate local pair-wise alignments of larger sequences

SYNOPSIS

supermatcher -asequence seqall -bsequence seqset [-datafile matrixf] [-minscore float] -gapopen float -gapextend float [-width integer] [-wordlen integer] -outfile align [-errorfile outfile]
supermatcher -help

DESCRIPTION

supermatcher

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 seqall

-bsequence seqset

-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.

-minscore float

: Minimum alignment score to report an alignment.

Required section

-gapopen float

: Default value: @($(acdprotein)? 10.0 : 10.0)

-gapextend float

: Default value: @($(acdprotein)? 0.5 : 0.5)

Additional section

-width integer

: Default value: 16

-wordlen integer

: Default value: 6

Output section

-outfile align

-errorfile outfile

: Error file to be written to for failed alignments Default value: supermatcher.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).

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.