water - Smith-Waterman local alignment of sequences
water -asequence sequence
-bsequence seqall
[-datafile matrixf]
-gapopen float
-gapextend float
-brief boolean
-outfile align
water -help
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).
-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.
-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)
-brief boolean
Brief identity and similarity Default value: Y
-outfile align
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).
water is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
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.