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    Methods for evaluating oligonucleotide probe sequences
    1.
    发明申请
    Methods for evaluating oligonucleotide probe sequences 审中-公开
    评估寡核苷酸探针序列的方法

    公开(公告)号：US20050027461A1

    公开(公告)日：2005-02-03

    申请号：US10877231

    申请日：2004-06-24

    申请人： Karen Shannon ,  Paul Wolber ,  Glenda Delenstarr ,  Peter Webb ,  Robert Kincaid

    发明人： Karen Shannon ,  Paul Wolber ,  Glenda Delenstarr ,  Peter Webb ,  Robert Kincaid

    IPC分类号： C12Q1/68 ,  G01N33/48 ,  G01N33/50 ,  G06F19/20 ,  G06F19/24 ,  G06F19/00

    CPC分类号： G16B25/00 ,  G16B40/00

    摘要： Methods are disclosed for predicting the potential of an oligonucleotide to hybridize to a target nucleotide sequence. A predetermined number of unique oligonucleotides is identified. The unique oligonucleotides are chosen to sample the entire length of a nucleotide sequence that is hybridizable with the target nucleotide sequence. At least one parameter that is independently predictive of the ability of each of the oligonucleotides of the set to hybridize to the target nucleotide sequence is determined and evaluated for each of the above oligonucleotides. A subset of oligonucleotides within the predetermined number of unique oligonucleotides is identified based on the evaluation of the parameter. Oligonucleotides in the subset are identified that are clustered along a region of the nucleotide sequence that is hybridizable to the target nucleotide sequence. The method may be carried out with the aid of a computer.

    摘要翻译： 公开了用于预测寡核苷酸与靶核苷酸序列杂交的潜力的方法。 鉴定出预定数量的唯一寡核苷酸。 选择独特的寡核苷酸来对可与靶核苷酸序列杂交的核苷酸序列的整个长度进行采样。 确定并评估每种上述寡核苷酸的至少一个独立地预测该组寡核苷酸与靶核苷酸序列杂交的能力的参数。 基于参数的评估来鉴定预定数量的唯一寡核苷酸内的寡核苷酸的子集。 鉴定了亚群中的寡核苷酸，其沿着与靶核苷酸序列可杂交的核苷酸序列的区域聚集。 该方法可以借助于计算机进行。

    Customized and dynamic association of probe type with feature extraction algorithms
    3.
    发明申请
    Customized and dynamic association of probe type with feature extraction algorithms 审中-公开
    探头类型与特征提取算法的定制和动态关联

    公开(公告)号：US20060247867A1

    公开(公告)日：2006-11-02

    申请号：US11414005

    申请日：2006-04-28

    申请人： Glenda Delenstarr ,  Peter Webb ,  Charles Troup ,  Jayati Ghosh ,  Christian Le Cocq.

    发明人： Glenda Delenstarr ,  Peter Webb ,  Charles Troup ,  Jayati Ghosh ,  Christian Le Cocq.

    IPC分类号： G06F19/00

    CPC分类号： G16B50/00 ,  G16B25/00 ,  G16B40/00 ,  G16B45/00

    摘要： Systems, methods and computer readable media for extracting data from features on a chemical array, using a feature extraction module including feature extraction algorithms configured to calculate characteristics of array features. A reference table is provided that associates probe names of probes contained on the array with at least one additional identifier. The reference table is accessible by the feature extraction module to convert any one of the at least one additional identifiers to the probe names, and the probe names to at least one of the at least one additional identifiers.

    摘要翻译： 使用包括被配置为计算阵列特征的特征的特征提取算法的特征提取模块来从化学阵列上的特征提取数据的系统，方法和计算机可读介质。 提供了一个参考表，将数组中包含的探测器的探测名称与至少一个附加标识符相关联。 所述参考表可由所述特征提取模块访问，以将所述至少一个附加标识符中的任一个转换为所述探测器名称，并将所述探测器名称转换为所述至少一个附加标识符中的至少一个。

    Automated feature extraction processes and systems
    4.
    发明申请
    Automated feature extraction processes and systems 审中-公开
    自动特征提取过程和系统

    公开(公告)号：US20060056671A1

    公开(公告)日：2006-03-16

    申请号：US10941501

    申请日：2004-09-15

    申请人： Jayati Ghosh ,  Christian Le Cocq. ,  Xiangyang Zhou ,  John Corson ,  Glenda Delenstarr ,  Charles Troup

    发明人： Jayati Ghosh ,  Christian Le Cocq. ,  Xiangyang Zhou ,  John Corson ,  Glenda Delenstarr ,  Charles Troup

    IPC分类号： G06K9/00 ,  G06K9/46 ,  C12M1/34

    CPC分类号： G06T7/00 ,  G06T2207/30072 ,  G16B25/00

    摘要： Methods, systems and computer readable media for automatically feature extracting array images in batch mode. At least two images to be feature extracted are loaded into a batch project, and the system automatically and sequentially feature extracts the images in the batch project. At least one of the images may be feature extracted based upon a different grid template or protocol than at least one other of the images. Methods, systems and computer readable media are provided to automatically feature extract a single array image having an identifier indicating that it is a multipack, multiple array image. A system provided for feature extracting array images in batch mode includes a user interface with a feature enabling a user to select images to be loaded into a batch project; and based upon the loaded images in the batch project, the system may automatically assign a grid template to each image loaded into the batch project. Further, the system may automatically assign a protocol to each image loaded into the batch project.

    摘要翻译： 方法，系统和计算机可读介质，用于以批处理模式自动特征提取阵列图像。 要将特征提取的至少两个图像加载到批处理项目中，并且系统自动并顺序地特征提取批处理项目中的图像。 可以基于与至少另一个图像不同的网格模板或协议来提取图像中的至少一个。 提供方法，系统和计算机可读介质以自动特征提取具有指示其是多包多重阵列图像的标识符的单个阵列图像。 提供用于以批处理模式提取阵列图像的特征的系统包括具有使得用户能够选择要加载到批处理项目中的图像的特征的用户界面; 并且基于批处理项目中加载的图像，系统可以自动将网格模板分配给加载到批处理项目中的每个图像。 此外，系统可以自动将协议分配给加载到批处理项目中的每个图像。

    Systems, tools and methods of assaying biological materials using spatially-addressable arrays
    5.
    发明申请
    Systems, tools and methods of assaying biological materials using spatially-addressable arrays 失效

    公开(公告)号：US20060246494A1

    公开(公告)日：2006-11-02

    申请号：US11400717

    申请日：2006-04-06

    申请人： Glenda Delenstarr

    发明人： Glenda Delenstarr

    IPC分类号： C12Q1/68 ,  C12M1/34

    CPC分类号： C12Q1/6837 ,  C40B40/00 ,  C12Q2565/514 ,  C12Q2565/133 ,  C12Q2537/137 ,  C12Q2523/101

    摘要： Systems, tools and methods of assaying biological material are used to perform complex sandwich hybridization assays. The tools used comprise biological solution probes that are customized for each assay. The solution probe comprises a first region for hybridizing to a probe, in a generic set of capture probes on a universal assay apparatus, and a second region for hybridizing to a target in a sample. The solution probe assembles the target to the assay apparatus by hybridizing the second region to the target and the first region to the capture probe. In array assays, one or more biological samples, having one or more targets per sample, can be multiplexed on the same universal array comprising the generic set of capture probes in an array pattern of features on the substrate. The customized solution probe addresses and assembles a predetermined target-sample combination onto the array at a corresponding capture probe address location. The systems, tools and methods have specificity and sensitivity by systematically providing a reduced likelihood of cross-hybridizations and intramolecular structures in the probes. Specificity and sensitivity of the assay are provided by the incorporation of a chemically modified monomer in the capture probe and a similarly modified monomer complement in the first region of the solution probe. The modified monomers preferentially hybridize with each other. When the probe and respective probe region are oligonucleotides, the complementary modified nucleotides have a reversed polarity relative to the polarity of the respective probe and probe region. The complementary reversed polarity nucleotides form a thermodynamically more stable hybridization to each other than a hybridization between the reversed polarity nucleotide and a complementary nucleotide whose polarity is not similarly reversed.

    System and methods for characterization of chemical arrays for quality control
    8.
    发明申请
    System and methods for characterization of chemical arrays for quality control 有权
    用于表征化学阵列以进行质量控制的系统和方法

    公开(公告)号：US20070027637A1

    公开(公告)日：2007-02-01

    申请号：US11192680

    申请日：2005-07-29

    申请人： Glenda Delenstarr ,  Jayati Ghosh ,  John Corson

    发明人： Glenda Delenstarr ,  Jayati Ghosh ,  John Corson

    IPC分类号： G01N31/00 ,  G06F19/00

    CPC分类号： G06F19/20 ,  Y10T436/25

    摘要： Systems, methods and computer readable media for characterizing a chemical array. At least one metric indicative of accuracy of location of features on the chemical array by a feature extraction process used to extract signals from features of the chemical array may be generated, as well as additional metrics adapted to identify errors caused by a particular process used in generating the signals on the array. A quality control report may be generated to contain at least one metric indicative of accuracy of location and said at least one additional metric. Customized quality control reports may be generated by providing for user selection of at least one metric adapted to identify errors caused by a particular process used in generating signals on a chemical array, from plurality of metrics, and including such selections in the quality control report generated. Systems, methods and computer readable media are provided for characterizing a chemical array by generating metrics adapted to identify errors caused by a particular process used in generating the signals on the array, generating a quality control report containing at least one of the metrics, and outputting the quality control report.

    摘要翻译： 用于表征化学阵列的系统，方法和计算机可读介质。 可以产生指示化学阵列上的特征位置精度的至少一个度量，其特征提取过程用于从化学阵列的特征提取信号，以及适于识别由特定方法使用的特定过程引起的错误的附加度量 在阵列上产生信号。 可以生成质量控制报告以包含指示位置的精确度和所述至少一个附加度量的至少一个度量。 定制的质量控制报告可以通过提供用户选择适于识别由用于从多个度量生成化学阵列上的信号的特定过程引起的错误的至少一个度量，并且在生成的质量控制报告中包括这样的选择 。 提供了系统，方法和计算机可读介质，用于通过产生适于识别由用于产生阵列上的信号的特定过程引起的错误的度量来表征化学阵列，生成包含度量的至少一个的质量控制报告，以及输出 质量控制报告。

    Methods and systems for facilitating analysis of feature extraction outputs
    10.
    发明申请
    Methods and systems for facilitating analysis of feature extraction outputs 审中-公开
    用于促进特征提取输出分析的方法和系统

    公开(公告)号：US20070255512A1

    公开(公告)日：2007-11-01

    申请号：US11413643

    申请日：2006-04-28

    申请人： Glenda Delenstarr ,  Charles Troup ,  John Corson ,  Andrew Payne ,  David Gordon

    发明人： Glenda Delenstarr ,  Charles Troup ,  John Corson ,  Andrew Payne ,  David Gordon

    IPC分类号： G06F19/00 ,  G06F17/40

    CPC分类号： G16B50/00 ,  G16B25/00

    摘要： Methods, systems and computer readable media for facilitating analysis of feature extraction outputs across multiple extractions. A feature extraction output of an extraction resulting from feature extraction of an array is inputted, and global statistics and array processing parameters are extracted from the feature extraction output. A table/file is populated with the extracted global statistics and array processing parameters of the extraction. The inputting, extracting and populating steps are repeated for at least one additional feature extraction output of another extraction, so that the table/file includes global statistics that can be readily cross-compared over multiple extractions with reference to a single table or file. Methods, systems and computer readable media are provided for setting threshold values for metrics that global statistics are provided for. An evaluation metric may be set by a user, based upon the threshold values set for the metrics. A metric set including the metrics and optionally one or more thresholds and optionally an evaluation metric may be stored and/or applied to additional global statistics for those metrics to evaluate the quality of one or more extractions. A set of reports are provided for facilitating analysis of feature extraction outputs across multiple extractions. A diagnostic tool is provided for identifying and diagnosing potential problems in feature extraction outputs.

    摘要翻译： 方法，系统和计算机可读介质，用于促进跨多次提取的特征提取输出的分析。 输入从阵列的特征提取产生的提取的特征提取输出，并从特征提取输出中提取全局统计和阵列处理参数。 用提取的全局统计数据和数组处理参数填充表/文件。 针对另一个提取的至少一个附加特征提取输出重复输入，提取和填充步骤，使得表/文件包括参考单个表或文件可以容易地通过多次提取进行交叉比较的全局统计。 提供了方法，系统和计算机可读介质，用于为为全球统计提供的度量设置阈值。 评估度量可以由用户基于针对度量设置的阈值来设置。 可以将包括指标和可选的一个或多个阈值以及可选的评估度量的度量值存储和/或应用于这些度量的附加全局统计量，以评估一个或多个提取的质量。 提供了一组报告，以便于跨多次提取的特征提取输出分析。 提供诊断工具用于识别和诊断特征提取输出中的潜在问题。