Recent Patents in Bioinformatics, September — October 2010
US Patent 7,822,556. Expression data analysis systems and methods. Inventors: Shreeram Akilesh, Derry Roopenian, Daniel Shaffer. Assignee: The Jackson Laboratory.
Describes methods and applications of global pattern recognition, including a system for analyzing the results of RT-PCR experiments. The system includes a set of self-normalizing housekeeping primers or oligonucleotides "and an algorithmic approach to normalizing expression data from all primers on the plate based on the reaction products of several of the self-normalizing gene primers oligonucleotides," according to the patent abstract.
US Patent 7,818,281. Computer software for visualizing recombination events in a group of individuals from recombination breakpoints and assignments in high density SNP genotyping data by generating a color-coded view for each individual chromosome and a whole genome view for the group. Inventors: Giulia Kennedy, Yaron Turpaz, Chun Zhang. Assignee: Affymetrix.
Protects a computer system for visualizing recombination events in a group of individuals. According to one aspect of the invention, high-density SNP genotype data is obtained from related individuals. A pedigree is created, haplotypes are reconstructed, and likely recombination breakpoints are identified with the use of publicly available computer programs. "A software tool is then used facilitate the visualization of the recombination events in the family," the patent abstract states.
US Patent 7,809,765. Sequence identification and analysis. Inventors: Scott Charles Evans, Thomas Stephen Markham, Andrew Soliz Torres. Assignee: General Electric.
Describes a method of analyzing a data series to identify sequences of interest. Specifically, the method generates a data structure that stores characteristics about sequences present in a data series. More than one heuristic is calculated for each sequence under review, and the heuristics associated with each sequence are evaluated to identify a sequence of interest.
US Patent 7,809,510. Positional hashing method for performing DNA sequence similarity search. Inventor: Aleksandar Milosavljevic. Assignee: IP Genesis.
Describes positional hashing, a method for detecting similarities between texts such as DNA sequences, amino acid sequences, and natural language. "The method is particularly well suited for large-scale comparisons such as that of mutual comparisons of millions of sequence fragments that result from mammalian-scale sequencing projects and for whole-genome comparisons of multiple mammalian genomes," the patent abstract states. Positional hashing involves breaking the sequence comparison problem "along its natural structure," solving the subproblems independently, and then collating the solutions into an overall result, according to the patent abstract.
US Patent 7,809,509. Comparative mapping and assembly of nucleic acid sequences. Inventor: Aleksandar Milosavljevic.
Discloses a method for assembling nucleic acid sequence fragments using information about their relative position inferred by comparison against a known sequence of a related nucleic acid. In addition, the method localizes fragments to bacterial artificial chromosomes and determines relative position of BACs using sequence comparison information. "The method utilizes the information about relative orientation, mutual distance, fragment localization to bacterial artificial chromosomes, and relative position of bacterial artificial chromosomes to constrain the assembly process, thus resulting in a more accurate assembly requiring fewer sequencing reactions," according to the patent abstract.
US Patent 7,805,282. Process, software arrangement and computer-accessible medium for obtaining information associated with a haplotype. Inventors: Will Casey, Thomas Anantharaman, Bhubaneswar Mishra. Assignee: New York University.
Describes a method, system, and software arrangement for reconstructing two haplotypes of a diploid individual from genotype data. The method is based on a procedure "that is nearly linear in the number of polymorphic markers examined, and is therefore quicker, more accurate, and more efficient than other population-based approaches," according to the patent abstract.
US Patent 7,805,254. System, method and computer program for non-binary sequence comparison. Inventor: Jeffrey Clark. Assignee: Bioinformatica.
Describes a system and method for performing non-binary comparison of biological sequences that includes a new measure, Ω0, which is "a non-binary counting measure" that obtains "substantially more information about sequences and comparisons between them than is gathered by conventional bioinformatics techniques," the patent abstract states.
US Patent 7,805,252. Systems and methods for designing and ordering polynucleotides. Inventors: Claes Gustafsson, Sridhar Govindarajan, Jon Ness, Alan Marco Villalobos, Jeremy Minshull. Assignee: DNA Twopointo.
Protects a computer systems for designing oligonucleotides. A set of sequence elements is defined in which each sequence element represents an amino acid sequence segment or a nucleic acid sequence segment. The set of sequence elements "collectively represent a designed nucleic acid sequence," and are displayed as icons "in a linear or a near-linear arrangement such that each respective icon … uniquely represents a corresponding sequence element in the set of sequence elements." An oligonucleotide selection module is then used to identify oligonucleotides in the designed nucleic acid sequence.
US Patent 7,803,587. Method for developing culture medium using genome information and in silico analysis. Inventors: Sang Yup Lee, Ho Nam Chang, Hyohak Song, Tae Yong Kim, Bo-Kyung Choi. Assignee: Korea Advanced Institute of Science and Technology.
Describes a method for developing a culture medium using genome information and in silico analysis. In one implementation, the method involves developing a "minimal synthetic medium," including the steps of constructing a metabolic network using the genome information of a prokaryotic or eukaryotic cell, removing metabolites from the constructed metabolic network, and conducting metabolic flux analysis using in silico simulation.