Secondary structure defining database and methods for determining identity and geographic origin of an unknown bioagent thereby

A method for providing bioagent characterizing information comprising:

• a) measuring or calculating with a mass spectrometer a plurality of molecular masses corresponding to a plurality of amplification products wherein the amplification products are obtained by amplification of at least one target sequence of a bioagent nucleic acid gene sequence using a primer pair said target sequence region comprising two conserved regions that are hybridizable with the primer pair and that flank a variable region that uniquely varies between bioagents;
• b) calculating base compositions from said molecular mass measurements wherein said base compositions identify the number of A residues, C residues, T residues, G residues, U residues, analogues thereof and mass tag residues thereof;
• c) interrogating a database stored on a computer readable medium with an identification query, wherein said identification query comprises comparison of the base composition data from step b) with said database;
• said database comprising base composition data calculated or measured for the target sequence regions for at least nineteen bioagents and each of the calculated or measured base compositions is indexed to bioagent characterizing information;
• and
• d) delivering from said database a response comprising bioagent characterization information generated by the comparison of said measured base compositions of step b) and the calculated or measured base compositions of step c) thereby identifying a bioagent associated with an amplification product of step a).