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

Here is a sample session with water:

% water tsw:hba_human tsw:hbb_human
Smith-Waterman local alignment.
Gap opening penalty [10.0]:
Gap extension penalty [0.5]:
Output alignment [hba_human.water]:

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. You can usually expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception occurs when one or both sequences are single reads with possible sequencing errors, in which case you should expect many single base gaps. You can obtain this result by setting the gap open penalty to zero (or a very low value) and using the gap extension penalty to control gap scoring.

[-outfile] (align)

Output alignment filename.

Optional qualifiers:

-datafile (matrix)

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.

Advanced qualifiers:

-[no]similarity (boolean)

Display percent identity and similarity.