water - Smith-Waterman local alignment of sequences
water -asequence sequence -bsequence seqall [-datafile matrixf]
-gapopen float -gapextend float -brief boolean -outfile align
water is a command line program from EMBOSS (“the European Molecular
Biology Open Software Suite”). It is part of the "Alignment:Local"
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.
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: @($(acdprotein)? 10.0 : 10.0)
The gap extension penalty is added to the standard gap penalty for
each base or residue in the gap. This is how long gaps are
penalized. Usually you will expect a few long gaps rather than many
short gaps, so the gap extension penalty should be lower than the
gap penalty. An exception is where one or both sequences are single
reads with possible sequencing errors in which case you would
expect many single base gaps. You can get this result by setting
the gap open penalty to zero (or very low) and using the gap
extension penalty to control gap scoring. Default value:
@($(acdprotein)? 0.5 : 0.5)
Brief identity and similarity Default value: Y
Bugs can be reported to the Debian Bug Tracking system
(http://bugs.debian.org/emboss), or directly to the EMBOSS developers
water is fully documented via the tfm(1) system.
Debian Med Packaging Team
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