sourCEntral - mobile manpages

pdf

SUPERMATCHER

NAME

supermatcher − Match large sequences against one or more other sequences

SYNOPSIS

supermatcher −asequence seqall −bsequence seqset [−datafile matrixf] −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.

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 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).

SEE ALSO

supermatcher 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

Copyright © 2007 Debian-Med Packaging Team

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.

pdf