Max Planck Institut of Molecular Plant Physiology

PROMI
PROfile analysis by Mutual Information

Pattern matching mode

Following citations are taken from the ps_scan documentation. For further information please visit the PROSITE help.

pattern greediness off (-g option)

A pattern matching engine is said to be "greedy" if it tries to extend at most variable-length pattern elements. The sequence "ABCDC" and the pattern "A-x(1,3)-C" will produce the match "ABCDC" with a greedy engine, and the match "ABC" with a non-greedy one. By default, PROSITE is scanned in greedy mode, unless the -g option is set.

overlaps (-v option) and included matches (-i option)

Some patterns may produce distinct but overlapping matches on a given sequence. Additionally, if the pattern contains variable-length elements, some of these matches may be completely included in another one. Different combinations of -g, -v and -i options may produce differences in match count and match positions with patterns that contain variable-length elements. An engine which allows overlaps should be greedy in order to reduce the number of multiple hits which are almost entirely overlapping except at the extremities.

Some helpfull examples

Use copy and paste, to evaluate the examples given below.

zinc finger C2H2 domain

x(7)-C-x(2,4)-C-x(3)-[LIVMFYWC]-x(8)-H-x(3,5)-H-x(7)

SNF1 Kinase family

.M.R..S...L|.L.K..S...F|.V.H..S...I|.FR...S...M|.I....S...V
(regular expression with alternatives)
/help.shtml last modified at 19. Aug 2008 through hummel@mpimp-golm.mpg.de