NAME

       water - Smith-Waterman local alignment of sequences

SYNOPSIS

       water -asequence sequence -bsequence seqall [-datafile matrixf] -gapopen float
             -gapextend float -brief boolean -outfile align

       water -help

DESCRIPTION

       water 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 seqall

       -datafile matrixf
           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.

   Required section
       -gapopen float
           The gap open penalty is the score taken away when a gap is created. The best value
           depends on the choice of comparison matrix. The default value assumes you are using
           the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide
           sequences. Default value: @($(acdprotein)? 10.0 : 10.0)

       -gapextend float
           The 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 open penalty to zero (or very low) and
           using the gap extension penalty to control gap scoring. Default value:
           @($(acdprotein)? 0.5 : 0.5)

   Output section
       -brief boolean
           Brief identity and similarity Default value: Y

       -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

       water 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.