WORDFINDER(1e) | EMBOSS Manual for Debian | WORDFINDER(1e) |
NAME¶
wordfinder - Match large sequences against one or more other sequencesSYNOPSIS¶
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 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 seqset -bsequence seqall -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.
Required section¶
-gapopen floatDefault value: @($(acdprotein)? 30.0 :
30.0)
-gapextend float
Default value: @($(acdprotein)? 1.5 :
1.5)
Additional section¶
-width integerDefault value: 16
-wordlen integer
Default value: 6
-limitmatch integer
-limitalign integer
-lowmatch integer
-lowalign integer
Output section¶
-outfile align -errorfile outfileError file to be written to Default value:
wordfinder.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¶
wordfinder 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 |