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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Using the B options (BN,BI,BF) on the menu you can control which pattern symbols will be used during the initial pattern search and during the refinement phase. In the pattern C-x(2)-[DE], C and [DE] are the symbols.

The pattern symbols that can be used, are read from a file if the BI option is set, otherwise a default set will be used.

The default set has as the 20 first elements, the single amino acid symbols, and it also contains a set of ambiguous symbols, each containing amino acids that share some physio-chemical properties

If BI is set, option BF will appear to allow you to give the name of the file. In the file each symbol is given on a separate line containing the letters that the symbol should match. For instance the file could be:

and only patterns with the symbols C and [DE] would be considered. During the initial search, pattern symbols corresponding to the first BN lines can be used. Increasing BN will slow down the search and increase the memory usage, but allow more ambiguous pattern symbols.

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