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.