MATCHER(1e) | EMBOSS Manual for Debian | MATCHER(1e) |
NAME¶
matcher - Waterman-Eggert local alignment of two sequencesSYNOPSIS¶
matcher
-asequence sequence
-bsequence sequence
[-datafile matrix]
[-alternatives integer]
[-gapopen integer]
[-gapextend integer]
-outfile align
matcher
-help
DESCRIPTION¶
matcher 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 sequence -bsequence sequence -datafile matrixThis 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.
Additional section¶
-alternatives integerThis sets the number of alternative matches
output. By default only the highest scoring alignment is shown. A value of 2
gives you other reasonable alignments. In some cases, for example multidomain
proteins of cDNA and genomic DNA comparisons, there may be other interesting
and significant alignments. Default value: 1
-gapopen integer
The gap penalty is the score taken away when a
gap is created. The best value depends on the choice of comparison matrix. The
default value of 14 assumes you are using the EBLOSUM62 matrix for protein
sequences, or a value of 16 and the EDNAFULL matrix for nucleotide sequences.
Default value: @($(acdprotein)? 14 : 16)
-gapextend integer
The gap length, or gap extension, penalty is
added to the standard gap penalty for each base or residue in the gap. This is
how long gaps are penalized. Usually you will expect a few long gaps rather
than many short gaps, so the gap extension penalty should be lower than the
gap penalty. An exception is where one or both sequences are single reads with
possible sequencing errors in which case you would expect many single base
gaps. You can get this result by setting the gap penalty to zero (or very low)
and using the gap extension penalty to control gap scoring. Default value:
@($(acdprotein)? 4 : 4)
Output section¶
-outfile alignBUGS¶
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¶
matcher 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 |