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BioInform s Patent Roundup: Recent Patents in Bioinformatics: Feb 7, 2005

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US Patent 6,850,876. Cell based binning methods and cell coverage system for molecule selection. Inventors: Raymond Lam, William Welch, Sidney Young. Assignee: Smithkline Beecham (Now GlaxoSmithKline).

Protects a cell-based or data-driven binning method for providing a representative set of compounds to screen in high-throughput screening. The method allows the inclusion of all molecules, generates a high percentage of occupied cells, and provides adequate division of the molecules in the low-dimensional subspaces. A chemical space coverage criterion measures the uniformity of coverage of the molecules selected, and a fast exchange design algorithm minimizes the number of searches of the candidate points while maximizing the number of exchanges during each pass through the candidate points. According to the inventors, this method “is many times faster than previous exchange algorithms and generates designs with good coverage properties.”


US Patent 6,850,846. Computer software for genotyping analysis using pattern recognition. Inventors: Eugene Wang, Teresa Webster. Assignee: Affymetrix.

Protects methods, systems, and computer software products for determining the genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call. The methods include obtaining a plurality of sample-probe intensities reflecting the hybridization between the sample and a plurality of probes; determining a tentative genotype based upon the sample probe intensities; and accepting the tentative genotype as the genotype of the sample if the pattern of the sample probe intensities is similar to that of reference probe intensities for the tentative genotype. Preferred methods for determining the similarity of probe intensity patterns include evaluating the linear correlation coefficient between probe intensities, and accepting the tentative genotype as the genotype of the sample if the linear correlation coefficient is greater than a threshold value, which may be at least 0.8, 0.9, or 0.95.


US Patent 6,847,897. Method and system for analyzing biological response signal data. Inventors: Douglas Bassett, Andrey Bondarenko. Assignee: Rosetta Inpharmatics.

Covers a system, method, and computer program product for computer-aided analysis of biological response data. In a preferred embodiment, biological datasets are graphically selected by a user from a first active biological viewer window on a user computer display and projected onto one or more other active biological viewers on the display. The selected data is highlighted in destination biological viewers using contrast or color differentiation from other data appearing in the destination windows. In another preferred embodiment, hierarchical cluster trees from biological signal profiles are presented in a hyperbolic display fashion. In another preferred embodiment, biological menu and submenu items utilized by the user computer are not stored in the user computer, but are stored a central biological response database. Biological menus and submenus are generated at startup time based on queries to the central biological response database, “allowing for increased flexibility, changeability, and customization of the biological menus,” according to the inventors. In another preferred embodiment, correlation data between biological signal profile data is pre-computed when the experiments are added to the central biological response database, eliminating the need for real-time computation of correlation coefficients by the user computer.


US Patent 6,842,703. Profile searching in nucleic acid sequences using the fast Fourier transformation. Inventor: William Newell. Assignee: Aventis Pharmaceuticals.

Covers computer-implemented methods for detecting known blocks of functionally aligned protein sequences in a test nucleic acid sequence, such as an uncharacterized EST. The method includes several steps, including reverse-translating the set of protein sequences to a set of functionally aligned nucleic acid sequences using codon-usage tables and creating a profile from the set of functionally aligned nucleic acid sequences; constructing a first indicator function for the profile and a second indicator function for the test nucleic acid sequence; and computing the Fourier transform of each of the indicator functions. The method sums the Fourier transforms of the number of matches for each base to obtain the total Fourier transform.

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