seqmatchall does an all-against-all pairwise comparison of words (fragments of the sequences of a specified fixed size) in a set of sequences and finds regions of similarity within any two sequences.

Here is a sample session with seqmatchall. We use an increased word size to avoid accidental matches:

% seqmatchall Does an all-against-all comparison of a set of sequences Input sequence set: embl:eclac* Word size [4]: 15 Output file [outfile.seqmatchall]:

Mandatory qualifiers:

[-sequence] (seqset)

Sequence set USA.

-wordsize (integer)

Word size.

[-outfile] (outfile)

Output filename.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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