Secondary structure defining database and methods for determining identity and geographic origin of an unknown bioagent thereby
First Claim
1. 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 region of a bioagent nucleic acid gene sequence using a primer pair that hybridizes to the at least one target sequence region of a plurality of bioagents;
said target sequence region comprising two conserved regions wherein a first conserved region is hybridizable with a first primer of the primer pair and a second conserved region is hybridizable with a second primer of the primer pair, and wherein the two conserved regions flank a variable region that uniquely varies between said plurality of bioagents;
b) interrogating a database stored on a computer readable medium with an identification query, wherein said identification query comprises comparison of the measured molecular mass data of step a) with said database;
said database comprising molecular masses calculated or measured for the target sequence regions for a plurality of bioagents and each of the calculated or measured molecular masses is indexed to bioagent characterizing information; and
c) delivering from said database a response comprising bioagent characterizing information generated by the comparison of said measured molecular masses of step a) and said calculated or measured molecular masses of step b) thereby identifying a bioagent associated with an amplification product of step a).
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Abstract
The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further relates to methods for interrogating a database as a source of molecular masses of known bioagents for comparing against the molecular mass of an unknown or selected bioagent to determine either the identity of the selected bioagent, and/or to determine the origin of the selected bioagent. The identification of the bioagent is important for determining a proper course of treatment and/or irradication of the bioagent in such cases as biological warfare. Furthermore, the determination of the geographic origin of a selected bioagent will facilitate the identification of potential criminal identity.
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Citations
13 Claims
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1. 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 region of a bioagent nucleic acid gene sequence using a primer pair that hybridizes to the at least one target sequence region of a plurality of bioagents;
said target sequence region comprising two conserved regions wherein a first conserved region is hybridizable with a first primer of the primer pair and a second conserved region is hybridizable with a second primer of the primer pair, and wherein the two conserved regions flank a variable region that uniquely varies between said plurality of bioagents;
b) interrogating a database stored on a computer readable medium with an identification query, wherein said identification query comprises comparison of the measured molecular mass data of step a) with said database;
said database comprising molecular masses calculated or measured for the target sequence regions for a plurality of bioagents and each of the calculated or measured molecular masses is indexed to bioagent characterizing information; and
c) delivering from said database a response comprising bioagent characterizing information generated by the comparison of said measured molecular masses of step a) and said calculated or measured molecular masses of step b) thereby identifying a bioagent associated with an amplification product of step a). - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
- 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 region of a bioagent nucleic acid gene sequence using a primer pair that hybridizes to the at least one target sequence region of a plurality of bioagents;
Specification