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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When the R option is switched on, patterns found during the initial pattern search are input to a refinement algorithm where more ambiguous pattern symbols can be added.
For instance the pattern

might be refined to

If the RG option is switched on, then ambiguous symbols listed in the symbols file (or in the default symbol set -- see help for option B), are used. If RG is off, only the letters needed to match the input sequences are included in the ambiguous pattern positions.

For example, if [ILV] is a listed allowed symbol, and [IL] is not, [IL] can be included in a pattern if RG is off, but if RG is on, the full symbol [ILV] will be included instead.

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