Ptof converts a protein profile (generated for instance by pftools programs pfmake, gtop or htop) into a so-called 'frame-search profile'. A frame-search profile is used to search an 'interleaved frame-translated' DNA sequence (generated by pftools program 2ft) for occurrences of a protein sequence motif. An 'interleaved frame-translated' DNA sequence is an amino acid sequence corresponding to the N-2 overlapping codons of a DNAsequence of length N. Note that in such a sequence, the character *O* is used to represent stop codons. The conversion procedure works as follows: The protein profile is expanded in length by a factor of three to accommodate three translated codons per original match position. Two dummy match positions are placed between two consecutive significant match positions imported from the original profile. The original insert positions are placed between pairs of adjacent dummy match positions. The initiation, termination, and transition scores of the original insert positions are left unchanged; the insert extension scores are divided by a factor of 3, or by the value of the command-line option -I. The two insert positions flanking the significant match positions serve to accommodate frame-shift errors and introns, respectively. The frame-shift insert position allows free insertion opening combined with a high insert extension penalty (command-line option -F) whereas the intron insertion position has high opening but low extension penalties (command line options -Y and -Z). The deletion opening and closing penalties next to the significant match positions are set to values that ensure that the total cost of a single-base deletion is the same as the cost of a single base-insertion at a frame-shift insert position. Furthermore, the alphabet of the original profile is extended by the stop codon symbol *O* which is assigned a constant negative value (command-line option -X) at significant match positions, and zero at dummy match positions. At insert positions, it is set to the average of the other insert extension scores.
Parent program: pftools
PFTools is a collection of programs supporting the generalized profile format and search method of PROSITE.