NAME¶
matcher - Waterman-Eggert local alignment of two sequences
SYNOPSIS¶
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¶
-asequence sequence
-bsequence sequence
-datafile matrix
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.
Additional section¶
-alternatives integer
This 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 align
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.
