Computer-aided visualization and analysis system for sequence evaluation
AssigneeAffymetrix, Inc.
InventorsMark S. Chee, Chunwei Wang, Luis C. Jevons, Derek H. Bernhart, Robert J. Lipshutz
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Abstract
A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3).
Claims35
In a computer system, a method of identifying an unknown base in a sample nucleic acid sequence, said method comprising the steps of:
- inputting a plurality of probe intensities, each of said probe intensities being associated with a nucleic acid probe;
- said computer system comparing said plurality of probe intensities wherein each of said plurality of probe intensities is substantially proportional to said associated nucleic acid probe hybridizing with at least one nucleic acid sequence, said at least one nucleic acid sequence including said sample sequence;
- and
- calling said unknown base according to results of said comparing step.
In a computer system, a method of identifying an unknown base in a sample nucleic acid sequence, said method comprising the steps of:
- inputting a plurality of probe intensities, each of said probe intensities being associated with a nucleic acid probe;
- said computer system comparing said plurality of probe intensities wherein each of said plurality of probe intensities is substantially proportional to said associated nucleic acid probe hybridizing with said sample sequence;
- and
- calling said unknown base according to results of said comparing step.
In a computer system, a method of identifying an unknown base in a sample nucleic acid sequence, said method comprising the steps of:
- inputting a first set of probe intensities, each of said probe intensities in said first set being associated with a nucleic acid probe and substantially proportional to said associated nucleic acid probe hybridizing with a reference nucleic acid sequence;
- inputting a second set of probe intensities, each of said probe intensities in said second set being associated with a nucleic acid probe and substantially proportional to said associated nucleic acid probe hybridizing with said sample sequence;
- said computer system comparing at least one of said probe intensities in said first set and at least one of said probe intensities in said second set;
- and
- calling said unknown base according to results of said comparing step.
In a computer system, a method of identifying an unknown base in a sample nucleic acid sequence, said method comprising the steps of:
- inputting statistics about a plurality of experiments, each of said experiments producing probe intensities each being associated with a nucleic acid probe and substantially proportional to said associated nucleic acid probe hybridizing with a reference nucleic acid sequence;
- inputting a plurality of probe intensities, each of said plurality of probe intensities being associated with a nucleic acid probe and substantially proportional to said associated nucleic acid probe hybridizing with said sample sequence;
- said computer system comparing at least one of said plurality of probe intensities with said statistics;
- and
- calling said unknown base according to results of said comparing step.
A method of processing first and second nucleic acid sequences, comprising the steps of:
- providing a plurality of nucleic acid probes;
- labeling said first nucleic acid sequence with a first marker;
- labeling said second nucleic acid sequence with a second marker;
- and
- hybridizing said first and second labeled nucleic acid sequences at the same time.
In a computer system, a method of identifying mutations in a sample nucleic acid sequence, said method comprising the steps of:
- inputting a first set of probe intensities, each of said probe intensities in said first set being associated with a nucleic acid probe and substantially proportional to said associated nucleic acid probe hybridizing with a reference nucleic acid sequence;
- inputting a second set of probe intensities, each of said probe intensities in said second set being associated with a nucleic acid probe and substantially proportional to said associated nucleic acid probe hybridizing with said sample sequence;
- said computer system comparing probe intensities in said first set and probe intensities in said second set to select hybridization regions where said probe intensities in said first set and said probe intensities in said second set differ;
- and
- identifying mutations according to characteristics of said selected regions.
In a computer system, a method of analyzing a plurality of sequences of bases, said plurality of sequences including at least one reference sequence and at least one sample sequence, the method comprising the steps of:
- displaying said at least one reference sequence in a first area on a display device;
- and
- displaying said at least one sample sequence in a second area on said display device;
- whereby a user is capable of visually comparing said plurality of sequences.
Dependencies are inferred from the claim text.