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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F Options:

The F options control flexible wildcards in the patterns:

Option FN:Using this option you can set the maximum number of flexible wildcards (matching a variable number of arbitrary sequence symbols). For instance x(2,4) is a flexible wildcard, and the patternC-x(2,4)-[DE]-x(10)-Fcontains one flexible wildcard.

Increasing FN will increase the time used by Pratt.

Option FL:

you can set the maximum flexibility of a flexible wildcard (matching a variable number of arbitrary sequence symbols). For instance x(2,4) and x(10,12) has flexibility 2, and x(10) has flexibility 0. Increasing FL will increase the time used by Pratt.

Option FP:

Using option FP you can set an upper limit on the product of a flexibilities for a pattern. This is related to the memory requirements of the search, and increasing the limit, increases the memory usage. Some patterns and the corresponding product of flexibilities:

C-x(2,4)-[DE]-x(10)-F - (4-2+1)*(10-10+1)= 3

C-x(2,4)-[DE]-x(10-14)-F - (4-2+1)*(14-10+1)= 3*5= 15

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Tuesday 12 February, 2008