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

• US 20040122857A1
• Filed: 12/18/2002
• Published: 06/24/2004
• Est. Priority Date: 12/18/2002
• Status: Abandoned Application

• Current Assignee: Ibis Biosciences Incorporated
• Original Assignee: Ibis Biosciences Incorporated
• Inventors: Crooke, Stanley T., Sampath, Rangarajan, McNeil, John, Ecker, David J., Hofstadler, Steven, Griffey, Richard
• Application Number:
  US10/326,643
• Publication Number:
  US 20040122857A1
• Time in Patent Office: Days
• US Class Current: 707/104.1
• CPC Class Codes: G16B 15/00 ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
• CPC Class Codes: G16B 15/10 Nucleic acid folding
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/20 Heterogeneous data integration

Abstract

The present invention relates generally to the field of investigational bioinformatics and more particularly to secondary structure defining databases. The present invention further elates 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.

Claims

1. A database having cell-data positional significance comprising at least a first table of a plurality of data-containing cells, said first table organized into at least a first row and a second row, each row having columns and data-containing cells;

and wherein said data-containing cells have an alignment with at least one other row for differentiating aligned from non-aligned data-containing cells, and wherein said differentiation in alignment of said data-containing cells designates a geographic feature of a polymer present in a sample.

2. The database according to claim 1 wherein said alignment is a vertical alignment according to base pair homology along a linear segment within each polymer.

3. The database according to claim 1 wherein said vertical alignment further aligns cell-data according to inter-species conserved regions.

4. The database according to claim 1 wherein the geographic feature is an origin of a bioagent.

5. The database according to claim 1 wherein the polymer is an RNA.

6. A service providing information related to the geography of a bioagent in a sample comprising:

providing a dimensional master database for storing a molecular mass, an identity and a geographic detail corresponding to a plurality of known bioagents and, said master database storing the molecular mass, the identity and the geographic detail for a plurality of known bioagents;

interrogating the master database with an identification request of an unknown bioagent in a sample to generate a response; and

delivering said response from the master database to a requester.

7. The service according to claim 6 wherein the molecular mass is of a selected portion of the known bioagent, the identity comprises at least a name for the known bioagent, and the geographic detail comprises at least a geographic origin, geographic distribution, or treatment.

8. The service according to claim 6 wherein the request comprises a symptomatology and the identification comprises a recommended pair of primers for hybridizing to sequences of nucleic acid flanking a variable nucleic acid sequence of the unknown bioagent, and said pair of primers are hybridized to the sequences of nucleic acid flanking a variable nucleic acid sequence of the unknown bioagent.

9. The service according to claim 8 wherein the nucleic acid sequence of the unknown bioagent between said pair of primers defines the selected portion of both the known bioagents and the unknown bioagent.

10. The service according to claim 9 wherein the response is delivered through a network.

11. The service according to claim 9 wherein the request comprises a molecular mass of the unknown bioagent for the selected portion and where the response generated thereto comprises a set of molecular masses for analogous selected portions of know bioagents, and said set comprising at least one molecular mass from the master database.

12. The service according to claim 10 wherein the network is a local area network.

13. The service according to claim 10 wherein the network is a wide area network.

14. The service according to claim 11 wherein the network is the internet.