Nucleic acid analysis
AssigneeHelicos BioSciences Corporation
InventorLee Kamentsky
Life of this patent
Estimating the term…
Abstract
A sample nucleic acid sequence is compared against a database to find a matching sequence. In one embodiment, this comparison is accomplished with a table look-up approach that involves using sequences with collapsed homopolymer regions.
Claims18
A method of comparing nucleic acid sequences, comprising:
- providing a nucleic acid sequence obtained from a sample and including at least one homopolymer region;
- collapsing each of the homopolymer regions to a single nucleotide to form a representative sample sequence without homopolymer regions;
- and
- comparing the representative sample sequence to at least one of a plurality of reference nucleic acid sequences without homopolymer regions to determine whether the representative sample sequence matches one of the plurality of reference nucleic acid sequences.
A method of comparing nucleic acid sequences, comprising:
- providing a nucleic acid sequence obtained from a sample and including at least one homopolymer region;
- collapsing each of the homopolymer regions to a single nucleotide to form a representative sample sequence without homopolymer regions;
- comparing the representative sample sequence to one or more members of a database of reference nucleic acid sequences without homopolymer regions to determine whether the representative sample sequence matches one of the reference nucleic acid sequences, at least one of the reference nucleic acid sequences created by collapsing at least one homopolymer region to a single nucleotide, the database comprising information that is related to the at least one reference nucleic acid sequence and that is indicative of one or more corresponding nucleic acid sequences in which no homopolymer region was collapsed;
- identifying one of the reference nucleic acid sequences in the database that matches the representative sample sequence;
- identifying, for the identified reference nucleic acid sequence and based on any related and indicative information for the identified reference nucleic acid sequence, any one or more corresponding nucleic acid sequences in which no homopolymer region was collapsed;
- and
- determining which of the identified corresponding nucleic acid sequences matches the nucleic acid sequence obtained from the sample.
A method of matching nucleic acid sequences, comprising:
- sequencing a nucleic acid from a patient;
- collapsing each homopolymer region of the patient nucleic acid sequence to a single nucleotide to form a representative sample sequence;
- and
- determining whether the representative sample sequence matches a member of a database of reference nucleic acid sequences without homopolymer regions, at least one of the reference nucleic acid sequences created by collapsing at least one homopolymer region to a single nucleotide, at least some of the reference nucleic acid sequences being indicative of a diagnosis, prognosis, or indication for a course of treatment of the patient.
A computer-readable medium storing a plurality of sequence representations, each of the sequence representations comprising a unique nucleic acid sequence without a homopolymer region, at least one of the sequence representations created by collapsing at least one homopolymer region to a single nucleotide.
Dependencies are inferred from the claim text.