supermatcher finds a match of a large sequence against one or more sequences.

Here is a sample session with supermatcher:

% supermatcher tembl:ec\* tembl:eclac -word 50 -sbegin2 101 -send2 -101
Finds a match of a large sequence against one or more sequences
Gap opening penalty [10.0]: 3.0
Gap extension penalty [0.5]:
Output alignment [eclac.supermatcher]:

Mandatory qualifiers:

[-seqa] (seqall)

Sequence database USA.

[-seqb] (seqset)

Sequence set USA.

-gapopen (float)

Gap opening penalty.

-gapextend (float)

Gap extension penalty.

-outfile (align)

Output alignment filename.

Optional qualifiers:

-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.

-width (integer)

Alignment width.

-wordlen (integer)

word length for initial matching.

-errorfile (outfile)

Error file to write to.