CBU - Computational Biology Unit

 
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.

Send an email to services@cbu.uib.no

P-options

P Options:

The P options are for controlling the patterns to be considered by Pratt. See also the F options for controlling flexibility.
Option PL:
Allows you to set the maximum length of a pattern. The length of the pattern C-x(2,4)-[DE] is 1+4+1=6. The memory requirement of Pratt depends on L; a higher L value gives higher memory requirement.
Option PN:
Using this you can set the maximum number of symbols in a pattern. The pattern C-x(2,4)-[DE] has 2 symbols (C and [DE]). When PN is increased, Pratt will require more memory.
Option PX:
Using this option you can set the maximum length of a wildcard. Examples of wildcards and lengths are
x - 1
x(10) - 10
x(3,4) - 4
Increasing PX will increase the time used by Pratt, and also slightly the memory required.

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

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