This is the command watere that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
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
Use watere online using onworks.net services
