matcher compares two sequences looking for local sequence similarities, using a rigorous algorithm.

Here is a sample session with matcher:

% matcher tsw:hba_human tsw:hbb_human
Finds the best local alignments between two sequences
Output file [hba_human.matcher]:

Here is an example to find the 10 best alignments:

% matcher tsw:hba_human tsw:hbb_human -alt 10
Finds the best local alignments between two sequences
Output file [hba_human.matcher]: hba_human.matcher10

Mandatory qualifiers:

[-sequencea] (sequence)

Sequence USA.

[-sequenceb] (sequence)

Sequence USA.

[-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.

-alternatives (integer)

This sets the number of alternative matches output. By default, only the highest scoring alignment is shown. A value of 2 gives you other reasonable alignments. In some cases (for example, multidomain proteins of cDNA and gemomic DNA comparisons) other interesting and significant alignments may be found.

-gappenalty (integer)

The gap penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value of 14 assumes you are using the EBLOSUM62 matrix for protein sequences, or a value of 16 and the EDNAFULL matrix for nucleotide sequences.

-gaplength (integer)

The gap length, or 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 would expect many single base gaps. You can obtain this result by setting the gap penalty to zero (or a very low value) and using the gap extension penalty to control gap scoring.