A brief introduction to PFMAKE
The program PFMAKE, belonging to PFTOOLS package, generates a PROSITE profile (generalized profile) from a multiple sequence alignment. The generalized profile syntax combines the functions of a variety of motif descriptors implemented in other methods, including regular expression-like patterns, weight matrices, "classical" profiles and certain types of hidden Markov models (HMM). A generalized profile can be used in homology detection by comparing a query profile against a DNA or protein sequence library.
For further details about generalized profiles and PFTOOLS package, see the ISREC Profile Homepage.

Availability in NPS@
PFMAKE is available :

First, you have to choose the weighting parameters : the number of shuffles per sequence to be performed, the total weight and the gap excision threshold (minimal fraction of non-gap characters a column of the multiple sequence alignment must contain in order to be considered for weighting). The weighting algorithm implemented corresponds to the method of Sibbald and Argos (1990).
Then you find the profile construction options: the alignment boundaries, the score matrix, the alignment mode, the block profile mode (this mode produces profiles that favor alignments with insertions and deletions positioned symmetrically around a few positions), the endgap and gap weighting modes and the circular profile mode.
Next you can set the profile construction parameters:

The scaling parameters (size of random database, upper and lower thresholds) don't have to be changed.

NPS@ PFMAKE output
The PFMAKE output allows you to follow your analysis with a profile search against a protein library thanks to PFSEARCH.