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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R-option

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
C-x(4)-D

might be refined to
C-x-[ILV]-x-D-x(3)-[DEF]

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.

This page is maintained by webmaster@bccs.uib.no. Last updated: Tuesday 12 February, 2008
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