Recent Patents in Bioinformatics, October — November 2010
US Patent 7,840,358. Hierarchical statistical framework for separating mixed data. Inventors: Nebojsa Jojic, Delbert Dwayne Dueck. Assignee: Microsoft.
The patent abstract describes a framework for separating mixed data, which facilitates, for example, "separating [DNA] sequencing data obtained from a mixture of two or more different sequences." According to the abstract, this method is "a shift from chaining hard-decision modules to an integrated soft-decision approach" and it further states that "sequencing data can be separated using machine-learning techniques to determine the correspondence between the sequencing data and the two or more different sequences."
US Patent 7,831,394. Information processing system using nucleotide sequence-related information. Inventors: Takamasa Kato, Takeo Morimoto. Assignee: Hitachi
Describes a system used to process information on nucleotide sequences. According to the patent abstract, the system obtains information representing a position in a nucleotide sequence in response to a request for an object and/or service and "evaluates the adequacy of transmission of nucleotide sequence-related information" that corresponds to the positional information obtained in the first step.
US Patent 7,831,392. System and process for validating, aligning and reordering one or more genetic sequence maps using at least one ordered restriction map. Inventors: Marco Antoniotti, Bhubaneswar Mishra, Thomas Anantharaman, Salvatore Paxia, David Schwartz. Assignee: Wisconsin Alumni Research Foundation
Describes an approach for comparing ordered segments of one DNA restriction map with ordered segments from a second map to determine the level of accuracy of one map with respect to the other, as well as a method for aligning multiple DNA sequences with an ordered DNA restriction map.
US Patent 7,826,979. Method of modeling complex formation between a query ligand and a target molecule. Inventors: Guy Bemis, Paul Caron, Brian Hare, Patrick Walters. Assignee: Vertex Pharmaceuticals
Describes computer-based approaches for modeling the interactions between a query ligand and a target macromolecule. According to the abstract, the methods can include providing structural models of the ligand and the macromolecule and identifying a substructure of the ligand. They also include "identifying comparison ligands in a set of 3D structural models that each share an identical substructure with the query ligand; mapping spatial relationships between the substructure atoms of the query ligand and the comparison ligand such that corresponding atoms are identified; assigning atomic coordinates to the corresponding atoms of the query ligand; and generating one or more output models."
US Patent 7,826,975. Method for redesign of microbial production systems. Inventors: Costas Maranas, Anthony Burgard, Priti Pharkya. Assignee: The Penn State Research Foundation.
The abstract describes a computer-assisted method for identifying functionalities to include in an organism-specific metabolic network that would enable a desired biotransformation in a host. This includes "accessing reactions from a universal database to provide stoichiometric balance, identifying at least one stoichiometrically balanced pathway [based] partially on the reactions and a substrate to minimize a number of non-native functionalities in the production host, and incorporating the at least one stoichiometrically balanced pathway into the host to provide the desired biotransformation."
US Patent 7,822,559. Methods and systems for detrending signal intensity data from chemical arrays. Inventors: John Frederick Corson, Jayati Ghosh, Svetlana Shchegrova. Assignee: Agilent Technologies.
Describes an approach for "removing trends in signal intensity values from features on a chemical array." According to the abstract, "inputted signal values from features on the array are surface fitted to calculate a surface approximation … [that] is normalized and used to de-trend the signal intensity values from the features."