US 7,623,997 B2Granted

Computer-implemented biological sequence identifier system and method

AssigneeThe United States of America as represented by the Secretary of the Navy

InventorsAnthony P. Malanoski, Baochuan Lin, Joel M Schnur, David A Stenger

Life of this patent

Estimating the term…

Loading patent…

Abstract

A method of: submitting reference sequences to a taxonomic database to produce taxonomic results; and reporting a taxonomic identification based on the taxonomic results. The reference sequences are the output of genetic database queries that return a score for each reference sequence. A method for processing a biological sequence obtained from an assay by: converting base calls located in a predetermined list of positions within the biological sequence to N; and determining the ratio of single nucleotide polymorphisms in the biological sequence relative to a reference sequence. Each entry in the predetermined list of positions represents the capability of a substance hybridizing to a microarray used to generate the biological sequence. The substance is not the nucleic acid of a target pathogen.

Claims8

Dependent claims

A method of processing a biological sequence representing a nucleotide sequence obtained from an assay comprising:

converting base calls located in a predetermined list of positions within the biological sequence to N;
wherein each entry in the predetermined list of positions represents the capability of a substance hybridizing to a microarray used to generate the biological sequence;
wherein the substance is not the nucleic acid of a target pathogen;
determining the ratio of single nucleotide polymorphisms in the biological sequence relative to a reference sequence;
selecting a potential subsequence of an initial length from the biological sequence, when the ratio of single nucleotide polymorphisms is below a SNP threshold;
and
calculating the ratio of unique base calls within the potential subsequence;
wherein the method is performed using a suitably programmed computer.

5 more elements

Dependencies are inferred from the claim text.

Facts

Application: 11/422,431Filed 6 Jun 2006 · continuation in part
Priority: 2 Jul 2004
Published: US 2007/0059728 A115 Mar 2007
Granted: 24 Nov 2009
Term ends: Not estimatedThe source records don’t support an estimate.

Classification8 codes

G16B 20/20
ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations: allele or variant detection, e.g. single…
G16B 30/00
Ict specially adapted for sequence analysis involving nucleotides or amino acids
G16B 30/10
ICT specially adapted for sequence analysis involving nucleotides or amino acids: sequence alignment; Homology search
G16B 20/00
Ict specially adapted for functional genomics or proteomics

Family

Application60/590,931Us provisional application · filed 2 Jul 2004
Application60/609,918Us provisional application · filed 15 Sep 2004
Application60/626,500Us provisional application · filed 5 Nov 2004
Application60/631,460Us provisional application · filed 29 Nov 2004
Application60/631,437Us provisional application · filed 29 Nov 2004
Application60/691,768Us provisional application · filed 16 Jun 2005
Application11/177,647Parent of this continuation-in-part · filed 2 Jul 2005
Application11/177,646Parent of this continuation-in-part · filed 2 Jul 2005
Application11/268,373Parent of this continuation-in-part · filed 7 Nov 2005
Application60/735,876Us provisional application · filed 14 Nov 2005
Application60/735,824Us provisional application · filed 14 Nov 2005
Application60/743,639Us provisional application · filed 22 Mar 2006
US 2007/0059728 A1Pre-grant publication · published 15 Mar 2007
US 2006/0210967 A1Published application
US 2007/0065832 A1Published application
US 2008/0020379 A1Published application
US 8,032,310 B2Related patent
US 7,623,997 B2This patent

From the US filing history. Foreign family members aren’t listed.