SUPERMATCHER(1e) | EMBOSS Manual for Debian | SUPERMATCHER(1e) |
NAME¶
supermatcher - Calculate approximate local pair-wise alignments of larger sequencesSYNOPSIS¶
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 matrixfThis 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 floatDefault value: @($(acdprotein)? 10.0 : 10.0)
-gapextend float
Default value: @($(acdprotein)? 0.5 : 0.5)
Additional section¶
-width integerDefault value: 16
-wordlen integer
Default value: 6
Output section¶
-outfile align -errorfile outfileError 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).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¶
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.05/11/2012 | EMBOSS 6.4.0 |