Pfmake builds a protein or DNA generalized profiles from a multiple sequence alignment. It generates a PROSITE profile from a multiple sequence alignment using methods described by Gribskov et al. (1990), Luethy et al. (1994), and Thompson et al. (1994), with modifications to exploit the features of the new profile format. The file containing the multiple sequence alignment (ms_file) must be either in MSF format as generated by GCG programs or by readseq (checksums are ignored) or in MSA format as created by psa2msa(1). If *-* is specified instead of a filename, the multiple sequence alignment is read from the standard input. The score_matrix file must also be in GCG format. If an already existing profile is given as input via the third optional argument, the parameters of the DISJOINT, NORMALIZATION and CUT_OFF blocks will be read from input, all other profile parameters will be recalculated. Header and footer lines outside the matrix block will also be transferred from input to output. If no input profile is given, the disjointness definition will be set to PROTECT with borders leaving short unpro- tected tails (maximum 5 positions) at the beginning and at the end of the profile. Furthermore, one normalization mode (n_score = raw_score or F where F is the output score multi- plier, see below), and two cut-off values (level 0: 8.5, level -1: 6.5) will be defined.
Parent program: pftools
PFTools is a collection of programs supporting the generalized profile format and search method of PROSITE.