Mean Recognition Score

Any functional DNA site may be formally characterized by a number of frequency matrices differing by the oligonucleotide
alphabet. That is why we have additionally designed the simplest procedure for the
simultaneous application of all available matrices of a given functional DNA site to
recognize this site within an arbitrary DNA sequence. For the fixed set {F_{1},
…, F_{q}, …, F_{Q}} of the Q frequency matrices having the Score_{0,q}(S)’s
calculated from a sequence S (see Partial Recognition Score),
the simplest simultaneous recognition procedure recommended by Decision-Making Theory
(Fishburn, 1970) is their arithmetically averaged recognition score:

where the recognition rule is the following:

__IF__ {Score_{S}(S)>0} __THEN__
{S is __this site__}, __OTHERWISE__ {S is not __this site__}.

Formula (4) is the most clear computational procedure for the simultaneous application of the several recognition procedures available. Due to this reason, we have especially chosen this simplest procedure (formula 4) to make the simultaneous recognition by a number of frequency matrices the most friendly for users who can, in this case, clearly understand how does it work.