Recent Patents in Bioinformatics, August — September 2010
US Patent No.7,797,302. Compiling co-associating bioattributes. Inventors: Andrew Kenedy, Charles Eldering. Assignee: Expanse Networks.
Presents a bioinformatics method, software, database, and system in which "attribute profiles of query-attribute-positive individuals and query-attribute-negative individuals are compared," and combinations of pangenetic and non-pangenetic attributes that occur at a higher frequency in the group of query-attribute-positive individuals are identified and stored to generate "a compilation of bioattribute combinations that co-associate with the query attribute," according to the patent abstract.
US Patent No.7,788,043. Methods, software arrangements and systems for aligning sequences which utilizes non-affine gap penalty procedure. Inventors: Ofer Gill, Yi Zhou, Bhubaneswar Mishra. Assignee: New York University.
Presents methods, software, and systems that can align DNA sequences "using piecewise-linear gap penalties that closely approximate general and biologically meaningful gap-functions," according to the patent abstract.
US Patent No.7,783,428. Methods, systems, and software for identifying functional biomolecules. Inventors: Claes Gustafsson, Sridhar Govindarajan, Robin Emig, Richard Fox, Ajoy Roy, Jeremy Minshull, S. Christopher Davis, Anthony Cox, Phillip Patten, Linda Castle, Daniel Siehl, Rebecca Gorton, Teddy Chen. Assignee: Maxygen.
Covers methods of rapidly and efficiently searching biological data space in order to identify biomolecules with desired properties, or which are most suitable for acquiring such properties, from complex libraries. The invention also provides methods of modeling sequence-activity relationships. "As many of the methods are computer-implemented, the invention additionally provides digital systems and software for performing these methods," the abstract states.
US Patent No.7,774,185. Protein structure alignment using cellular automata. Inventor: Deepak Gangadhar. Assignee: International Business Machines.
Describes a method for detecting protein sequence alignments that first generate protein blocks having a number of successive C-alpha atoms from two protein sequences and then determines a matrix of the distance of protein atoms from the C-alpha atoms for each block. A difference matrix represents the differences between the protein blocks of the two protein structures and a cellular automaton model is then generated in an initial configuration based upon the difference matrix, and evolved through at least one generation using predetermined rules.
US Patent No.7,774,182. Apparatus and method for validating a computer model. Inventor: Thomas Paterson. Assignee: Entelos.
Describes an apparatus and method for validating a computer model. In one embodiment, a computer-readable medium associates a set of configurations of a computer model with a stimulus-response test, and each configuration represents a different model scenario. The computer-readable medium applies the stimulus-response test to the set of configurations to produce a simulated response for each configuration and then compares the simulated responses for the set of configurations with an expected response to the stimulus-response test.
US Patent No.7,774,144. System and method for identifying complex patterns of amino acids. Inventors: Samuel Bogoch, Elenore Bogoch, Anne Borsanyi, Samuel Bogoch. Assignee: None.
Presents a method and system for identifying complex patterns in an amino acid sequence stored in a computer file or database. According to one aspect of the invention, the method can facilitate queries of protein databases by scanning received protein descriptions to identify and locate "Replikin patterns," which are sequences of between 7 and 50 amino acids, in which the sequence has at least one lysine residue located six to ten amino acid residues from a second lysine residue, the sequence has at least one histidine residue, and at least 6 percent of the amino acids in the sequence are lysine residues.
US Patent No.7,769,576. Method and apparatus for integrated modeling, simulation and analysis of chemical and biological systems having a sequence of reactions, each simulated at a reaction time determined based on reaction kinetics. Inventors: Ricardo Paxson, Joseph Hicklin. Assignee: The MathWorks.
Describes a system for modeling, simulating, and analyzing chemical and biochemical reactions that includes a modeling environment for constructing a model of a chemical or biochemical system comprising a plurality of chemical reactions.
US Patent No.7,761,239. Method of diagnosing biological states through the use of a centralized, adaptive model, and remote sample processing. Inventors: Tzong-Hao Chen, Ben Hitt, Peter Levine. Assignee: Correlogic Systems.
Presents a method for developing a model of a particular biological state that can be used to determine if an unknown biological sample exhibits a particular biological state. "Various business relationships may be developed to undertake various steps of the overall method for providing a diagnosis to a patient," the patent abstract states.