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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.



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