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Recent Patents in Bioinformatics, February — March, 2008

US Patent 7,343,249. Vectorization of sequence alignment computation using distance matrix reshaping. Inventors: Andre Heilper, Dmitry Markman. Assignee: International Business Machines.
Covers a method for comparing data sequences that includes accepting first and second data sequences of data elements, computing a distance matrix that includes rows and columns of matrix elements, and describing distances between the data elements of the first sequence and the data elements of the second data sequence. The distance matrix is “reshaped” and the method calculates a best-score path through the reshaped matrix using vector operations, “so as to quantify a similarity between the first and second data sequences,” according to the patent abstract. In an embodiment of the method, “the first and second data sequences include DNA chains, the data elements represent types of DNA nucleotides, and calculating the best-score path includes evaluating a match between the DNA chains,” according to the patent claims.

US Patent 7,343,247. Methods of classifying drug responsiveness using multiparameter analysis. Inventors: Leroy Hood, Andrew Siegel. Assignee: The Institute for Systems Biology.
Protects a computational method of diagnosing a disease or a health state in an individual by comparing the expression level of a sample of molecules in a specimen from the individual with a health-associated reference expression region of the sample of molecules. The patent also protects a method of classifying a population by drug responsiveness.

US Patent 7,343,246. Spatial profiling of proteins using hydrophobic moments. Inventor: Benjamin Silverman. Assignee: International Business Machines.
Covers several procedures for spatially profiling proteins by using hydrophobic moments. In one procedure, a shape or profile of a curve of a second-order moment of hydrophobicity is determined. A second procedure involves determining one or more ratios, “such as the ratio of a distance at which the second order moment of hydrophobicity vanishes to the distance at which a zero-order moment of hydrophobicity vanishes,” according to the patent abstract. “These procedures can be combined to provide a good mathematical determination of whether a protein belongs to a particular class of proteins,” the abstract states.

US Patent 7,340,485. Information management system for biochemical information. Inventors: Pertteli Varpela, Meelis Kolmer. Assignee: Medicel Oy.
Describes an information-management system for biochemical information, which is in the form of data sets that contain variable values organized as rows and columns. The system comprises “a row description list, in a variable description language, of the rows in the variable value matrix; a column description list, in a variable description language, of the columns in the variable value matrix; and a fixed dimension description, in a variable description language, of one or more fixed dimensions that are common to all values in the variable value matrix,” according to the patent abstract, which adds that the matrix can be analyzed “with many commercially available data-mining tools, such as self-organizing maps or other clustering algorithms, that do not readily process dimensioned values.”

US Patent 7,337,071. Information processing system using base sequence-related information. Inventors: Takamasa Kato, Takeo Morimoto. Assignee: Hitachi.
Protects a system for processing information for providing semantic information “useful for each individual organism through effective utilization of differences in nucleotide sequence-related information among individual organisms,” according to the patent abstract. The system first obtains information representing a position in a nucleotide sequence, then evaluates the “adequacy of transmission of nucleotide sequence-related information corresponding to the positional information.”

US Patent 7,330,588. Image metrics in the statistical analysis of DNA microarray data. Inventors: Carl Brown, Paul Goodwin. Assignee: Applied Precision.
Protects statistical analysis methods for assessing microarray images. The method uses probability density distributions generated by pixel-by-pixel analysis of images to measure the precision with which spot intensities are determined. “Simple weighting schemes based on these probability distributions are effective in improving significantly the quality of microarray data as it accumulates in a multi-experiment database,” according to the inventors.

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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.