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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.



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