Abstract: An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.

Abstract: A compression method includes: measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises a plurality of measured values and the chemical event is indicative of a number of nucleotide incorporations in a genetic sequencing reaction; applying a first compression process to the waveform, the first compression process including a truncating of data corresponding to a portion of the waveform that is not related to nucleotide incorporations in the genetic sequencing reaction; and applying a second compression process to the waveform, the second compression process including a data substitution process that replaces at least a portion of the waveform with a plurality of coefficients representative of the portion of the waveform.

Abstract: An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.

Abstract: A compression method includes measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values; applying a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform; applying a keyframe delta compression to the frame-averaged data; forming a compressed data structure including a keyframe and calculated differences subsequent to the keyframe; and storing one or more compressed data structures in memory.

Abstract: A compression method includes measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values; applying a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform; and applying a second compression process to the waveform, the second compression process including a truncating of data corresponding to a portion of the waveform that is not related to a nucleotide incorporation component of the waveform.

Abstract: A compression method includes: measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises a plurality of measured values and the chemical event is indicative of a number of nucleotide incorporations in a genetic sequencing reaction; applying a first compression process to the waveform, the first compression process including a truncating of data corresponding to a portion of the waveform that is not related to nucleotide incorporations in the genetic sequencing reaction; and applying a second compression process to the waveform, the second compression process including a data substitution process that replaces at least a portion of the waveform with a plurality of coefficients representative of the portion of the waveform.

Abstract: A method of estimating a parameter related to sequencing of a sample nucleic acid template includes: receiving signal data relating to nucleotide incorporation events resulting from a series of flows of nucleotides onto an array of wells including (i) a first well containing the sample nucleic acid template and (ii) a plurality of other sample-containing wells; determining sequence information for the sample nucleic acid template using signal data from the first well; and constructing a phase-state model for a set of nucleotide flows that contributed at least in part to the sequence information, wherein the model includes a signal correction parameter that is determined using signal data from the plurality of other sample-containing wells.

Abstract: Systems and methods for analyzing overlapping sequence information can obtain first and second overlapping sequence information for a polynucleotide, align the first and second sequence information, determine a degree of agreement between the first and second sequence information for a location along the polynucleotide, and determine a base call and a quality value for the location.

Abstract: A compression method includes measuring a waveform associated with a chemical event occurring on a sensor array, wherein the waveform comprises at least one region associated with expected measured values and at least one region associated with unpredictable measured values; applying a first compression process to the waveform, the first compression process including an averaging of one or more frames in one or more portions of the waveform; and applying a second compression process to the waveform, the second compression process including a truncating of data corresponding to a portion of the waveform that is not related to a nucleotide incorporation component of the waveform.

Abstract: A method for nucleic acid sequencing includes receiving a plurality of observed or measured signals indicative of a parameter observed or measured for a plurality of defined spaces; determining, for at least some of the defined spaces, whether the defined space comprises one or more sample nucleic acids; processing, for at least some of the defined spaces, the observed or measured signal to improve a quality of the observed or measured signal; generating, for at least some of the defined spaces, a set of candidate sequences of bases for the defined space using one or more metrics adapted to associate a score or penalty to the candidate sequences of bases; and selecting the candidate sequence leading to a highest score or a lowest penalty as corresponding to the correct sequence for the one or more sample nucleic acids in the defined space.

Abstract: An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.

Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.

Abstract: A method for nucleic acid sequencing includes receiving a plurality of signals indicative of a parameter measured for a plurality of defined spaces, at least some of the defined spaces including one or more sample nucleic acids, the signals being responsive to a plurality of nucleotide flows introducing nucleotides to the defined spaces; determining, for at least some of the defined spaces, whether the defined space includes a sample nucleic acid; processing, for at least some of the defined spaces determined to include a sample nucleic acid, the received signals to improve a quality of the received signals; and predicting a plurality of nucleotide sequences corresponding to respective sample nucleic acids for the defined spaces based on the processed signals and the nucleotide flows.

Abstract: An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.

Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.

Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.

Abstract: The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

Abstract: Methods and software products for analysis of alternative splicing are disclosed. In general the methods involve normalizing probe set or exon intensity to an expression level measurement of the gene. The methods may be used to identify tissue-specific alternative splicing events.

Abstract: The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

Abstract: An embodiment of a method of analyzing data from processed images of biological probe arrays is described that comprises receiving a plurality of files comprising a plurality of intensity values associated with a probe on a biological probe array; normalizing the intensity values in each of the data files; determining an initial assignment for a plurality of genotypes using one or more of the intensity values from each file for each assignment; estimating a distribution of cluster centers using the plurality of initial assignments; combining the normalized intensity values with the cluster centers to determine a posterior estimate for each cluster center; and assigning a plurality of genotype calls using a distance of the one or more intensity values from the posterior estimate.