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

   Input section
       -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

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

       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.