go to
> tfm(1)
Homepage > Man Pages > Category > General Commands
Homepage > Man Pages > Name > W

water

man page of water

water: Smith-Waterman local alignment of sequences

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 (//bugs.debian.org/emboss), or directly to the EMBOSS developers (//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. WATER(1)
 
 
 

Copyright © 2011–2018 by topics-of-interest.com . All rights reserved. Hosted by all-inkl.
Contact · Imprint · Privacy

Page generated in 13.08ms.

HTML Referenz | plr.li | uhren.name