CBU - Computational Biology Unit
The Pratt program is able to discover patterns conserved in sets of unaligned protein sequences. The output is in the form of Prosite patterns.

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Allows the use of an alignment or a query sequence to restrict the pattern search.

If G is set to al or query, another option GF will appear allowing the user to give the name of a file containing a multiple sequence alignment (in Clustal W format), or a query sequence in FastA format (without annotation).n Only patterns consistent with the alignment/matching the query sequence will be considered.

Loosely a pattern is considered consistent with the alignment if

-each symbol in the pattern (e.g. A) corresponds to a ungapped column in the alignment where all the characters match the pattern symbol (in the example, A).
-the wildcards in the pattern are compatible with the number of residues between the corresponding columns in the alignment.

For instance the pattern A-x(2,3)-B is consistent with the alignment

For more details see I. Jonassen
Efficient discovery of conserved patterns using a pattern graph.
Submitted to CABIOS

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