EMBOSS: water

Program water

Function

Smith-Waterman local alignment

Description

Uses the smith-waterman algorithm (modified for speed enhancments) to calculate the local alignment.

Usage

Here is a sample session with water. 

% water sw:hba_human sw:hbb_human
Gap opening penalty [10.0]: 
Gap extension penalty [0.5]: 
Output file [hba_human.water]: 

% more hba_human.water

Local: HBA_HUMAN vs HBB_HUMAN
Score: 293.50

HBA_HUMAN       2     LSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHF 46   
                      |:| :|: | | ||||  :  | | ||| |: : :| |: :|  |
HBB_HUMAN       3     LTPEEKSAVTALWGKV..NVDEVGGEALGRLLVVYPWTQRFFESF 45   

HBA_HUMAN       47    .DLS.....HGSAQVKGHGKKVADALTNAVAHVDDMPNALSALSD 85   
                       |||      |: :|| |||||  | :: :||:|::    : ||:
HBB_HUMAN       46    GDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHLDNLKGTFATLSE 90   

HBA_HUMAN       86    LHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLA 130  
                      ||  || ||| ||:|| : |:  || |   |||| | |:  | :|
HBB_HUMAN       91    LHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVA 135  

HBA_HUMAN       131   SVSTVLTSKY                                    140  
                       |:  |  ||
HBB_HUMAN       136   GVANALAHKY                                    145

Command line arguments 

   Mandatory qualifiers:
  [-sequencea]         sequence   Sequence USA
  [-seqall]            seqall     Sequence database USA
   -gapopen            float      Gap opening penalty
   -gapextend          float      Gap extension penalty
  [-outfile]           outfile    Output file name

   Optional qualifiers:
   -datafile           matrixf    Matrix file
   -showinternals      bool       Show internals

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default
[-sequencea]
(Parameter 1)		 Sequence USA Readable sequence Required
[-seqall]
(Parameter 2)		 Sequence database USA Readable sequence(s) Required
-gapopen Gap opening penalty Number from 1.000 to 100.000 10.0 for any sequence
-gapextend Gap extension penalty Number from 0.100 to 10.000 0.5 for any sequence
[-outfile]
(Parameter 3)		 Output file name Output file <sequence>.water
Optional qualifiers Allowed values Default
-datafile Matrix file Comparison matrix file in EMBOSS data path EBLOSUM62 for protein
EDNAMAT for DNA
-showinternals Show internals Yes/No No
Advanced qualifiers Allowed values Default
(none)

Input file format

Any two sequence USAs of the same type (DNA or protein).

Output file format

Data files

For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAMAT is used. Others can be specified.

EMBOSS data files are distributed with the application and stored in the standard EMBOSS data directory, which is defined by EMBOSS environment variable EMBOSS_DATA.

Users can provide their own data files in their own directories. Project specific files can be put in the current directory, or for tidier directory listings in a subdirectory called ".embossdata". Files for all EMBOSS runs can be put in the user's home directory, or again in a subdirectory called ".embossdata".

The directories are searched in the following order:

Notes

References

Warnings

Diagnostic Error Messages

Exit status

0 if successfull.

Known bugs

See also
Program nameDescription
matcherFinds the best local alignments between two sequences

Author(s)

This application was written by Alan Bleasby (ableasby@hgmp.mrc.ac.uk)

History 

Completed 7th July 1999.
Last modified 27th July 1999.

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments