## EMBOSS: water

# Program water

## Function

Smith-Waterman local alignment

## Description

water uses the Smith-Waterman algorithm (modified for speed enhancments) to calculate the local alignment.

The Smith-Waterman algorithm is a member of the class of algorithms that can calculate the best score and local alignment in the order of mn steps, (where 'n' and 'm' are the lengths of the two sequences). These dynamic programming algorithms were first developed for protein sequence comparison by Smith and Waterman, though similar methods were independently devised during the late 1960's and early 1970's for use in the fields of speech processing and computer science.

A local alignment searches for regions of local similarity between two sequences and need not include the entire length of the sequences. Local alignment methods are very useful for scanning databases or other circumsatnces when you wish to find matches between small regions of sequences, for example between protein domains.

Dynamic programming methods ensure the optimal local alignment by exploring all possible alignments and choosing the best. It does this by reading in a scoring matrix that contains values for every possible residue or nucleotide match. water finds an alignment with the maximum possible score where the score of an alignment is equal to the sum of the matches taken from the scoring matrix.

An important problem is the treatment of gaps, i.e., spaces inserted to optimise the alignment score. A penalty is subtracted from the score for each gap opened (the 'gap open' penalty) and a penalty is subtracted from the score for the total number of gap spaces multiplied by a cost (the 'gap extension' penalty).

Typically, the cost of extending a gap is set to be 5-10 times lower than the cost for opening a gap.

## 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]:

## Command line arguments

       Mandatory qualifiers:
      [-sequencea]         sequence   Sequence USA
      [-seqall]            seqall     Sequence database USA
       -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.
       -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.
      [-outfile]           align      (no help text) align value

       Optional qualifiers:
       -datafile           matrixf    Matrix file

       Advanced qualifiers:
       -[no]similarity     bool       Display percent identity and similarity

       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequencea] (Parameter 1) | Sequence USA | Readable sequence | Required
[-seqall] (Parameter 2) | Sequence database USA | Readable sequence(s) | Required
-gapopen | 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. | Number from 1.000 to 100.000 | 10.0 for any sequence

-gapextend

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.

Number from 0.100 to 10.000

0.5 for any sequence

[-outfile] (Parameter 3) | (no help text) align value | Alignment file |
Optional qualifiers | Allowed values | Default
-datafile | Matrix file | Comparison matrix file in EMBOSS data path | EBLOSUM62 for protein EDNAFULL for DNA
Advanced qualifiers | Allowed values | Default
-[no]similarity | Display percent identity and similarity | Yes/No | Yes

## Input file format

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

## Output file format

Here is the output file from the example run:

    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

    %id = 45.99                     %similarity = 64.23
    Overall %id = 43.15             Overall %similarity = 60.27

The %id is the percentage of identical matches between the two sequences over the reported aligned region.

The %similarity is the percentage of matches between the two sequences over the reported aligned region where the scoring matrix value is greater or equal to 0.0.

The Overall %id and Overall %similarity are calculated in a similar manner for the number of matches over the length of the longest of the two sequences.

## Data files

For protein sequences EBLOSUM62 is used for the substitution matrix. For nucleotide sequence, EDNAFULL 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:

- . (your current directory)
- .embossdata (under your current directory)
- ~/ (your home directory)
- ~/.embossdata

## Notes

water is a true implementation of the Smith-Waterman algorithm and so produces a full path matrix. It therefore cannot be used with genome sized sequences unless you have a lot of memory and a lot of time.

## References

1. Smith TF, Waterman MS (1981) J. Mol. Biol 147(1);195-7

## Warnings

Local alignment methods only report the best matching areas between two sequences - there may be a large number of alternative local alignments that do not score as highly. If two proteins share more than one common region, for example one has a single copy of a particular domain while the other has two copies, it may be possible to "miss" the second and subsequent alignments. You will be able to see this situation if you have done a dotplot and your local alignment does not show all the features you expected to see.

water is for aligning the best matching subsequences of two sequences. It does not necessarily align whole sequences against each other; you should use needle if you wish to align closely related sequences along their whole lengths.

A true Smith Waterman implementation like water needs memory proportional to the product of the sequence lengths. For two sequences of length 10,000,000 and 1,000 it therefore needs memory proportional to 10,000,000,000 characters. Two arrays of this size are produced, one of ints and one of floats so multiply that figure by 8 to get the memory usage in bytes. That doesn't include other overheads. Therefore only use water and needle for accurate alignment of reasonably short sequences.

If you run out of memory, try using supermatcher or matcher.

## Diagnostic Error Messages

    Uncaught exception
     Assertion failed
     raised at ajmem.c:xxx

Probably means you have run out of memory. Try using supermatcher or matcher if this happens.

## Exit status

0 if successful.

## Known bugs

None.

## See also

Program name | Description
--- | ---
matcher | Finds the best local alignments between two sequences
seqmatchall | Does an all-against-all comparison of a set of sequences
supermatcher | Finds a match of a large sequence against one or more sequences
wordmatch | Finds all exact matches of a given size between 2 sequences

matcher is a local alignment program that is less rigorous than

water

and therefore runs more quickly. It may be useful for database searching.

supermatcher is designed for local alignments of very large sequences and is even less rigorous in its implementation.

supermatcher Finds a match of a large sequence against one or more sequences matcher Finds 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.
    Modified 27th July 1999 - tweaking scoring.
    Modified 22 Oct 2000 - added ID and Similarity scores.

## Target users

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

## Comments