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Recent Patents in Bioinformatics, May — June 2007

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US Patent 7,231,390. Apparatus and method for providing sequence database comparison. Inventors: Douglas Blair, John Grefenstette, H. Hadon Nash, Dale Newfield, Dustin Lucien. Assignee: Parabon Computation.
 
Protects a method of comparing a query and a subject database using a distributed computing platform, according to the patent’s abstract. The databases are divided into data elements, and all data elements and task definitions are sent to a master CPU of a master-slave distributed computing platform. Data elements are sent to the slave CPUs for performance of the tasks and the results for each task are returned to a CPU.
 

 
US Patent 7,231,301. Method and a system for predicting protein functional site, a method for improving protein function, and a function-modified protein. Inventors: Hirofumi Doi, Hideaki Hiraki, Akio Kanai. Assignee: Japan Science and Technology Corporation.
 
Protects a method for predicting the functional site of a protein using the genome or cDNA data of an organism, according to the patent’s abstract. The method first calculates the frequency of occurrence of an oligopeptide in all the proteins of an organism, and then calculates the value of each amino-acid residue contributing to the frequency of occurrence as the representative value of the function. It predicts the protein functional site by using the representative value of function as an indicator.
 

 
US Patent 7,228,302. System, tools and methods for viewing textual documents, extracting knowledge therefrom and converting the knowledge into other forms of representation of the knowledge. Inventors: Allan Kuchinsky, Aditya Vailaya, David Moh, Peter Bluvas. Assignee: Agilent Technologies.
 
Covers systems, tools, methods, and recordable media for text-mining textual documents and extracting and associating entities and interactions mined with other data formats, such as diagrammatic displays and experimental data, according to the patent’s abstract. Additionally, information may be overlaid and compared with existing biological diagrams, the patent abstract states.
 

 
US Patent 7,228,238. Algorithmic design of peptides for binding and/or modulation of the functions of receptors and/or other proteins. Inventors: Arnold Mandell, Karen Selz, Michael Shlesinger. Assignee: Cielo Institute.
 
Covers a computational method for synthesizing a peptide or peptide-like molecule to a polypeptide or protein target, according to the patent’s abstract. The method is based on mode-matching each member of a set of peptide constituents of the peptide or peptide-like molecule to peptide constituents of the target polypeptide or protein target.
 

 
US Patent 7,226,732. Methods, apparatus, and computer programs for verifying the integrity of a probe. Inventors: Stanley Sakai, William McMillan. Assignee: Cepheid.
 
Protects methods and computer programs for verifying the integrity of a probe by comparing the fluorescence value of a probe to a threshold value, according to the patent’s abstract. The patent also describes methods for normalizing the fluorescence value of a probe and detecting a target nucleic acid in a sample.
 

 
US Patent 7,225,324. Multi-adaptive processing systems and techniques for enhancing parallelism and performance of computational functions. Inventors: Jon Huppenthal, David Caliga. Assignee: SRC Computers.
 
Protects “multi-adaptive processing systems and techniques for enhancing parallelism and performance of computational functions,” according to the patent abstract, according to the patent’s abstract. The methods can be employed in several applications, including multi-dimensional pipeline computations for seismic applications, search algorithms, information security, chemical and biological applications.
 

 
US Patent 7,225,183. Ontology-based information management system and method. Inventor: Steve Gardner. Assignee: IPXL.
 
Covers an information management system for integrating structured and unstructured data using an ontological approach, according to the patent’s abstract. The method also includes processes for creating, validating, augmenting, and combining ontologies for life science informatics and other disciplines, according to the patent abstract.
 

 
US Patent 7,217,509. Databases of regulatory sequences; methods of making and using same. Inventors: Alan Wolffe, Fyodor Urnov. Assignee: Sangamo Biosciences.
 

Protects methods and compositions for identifying, isolating, and characterizing regulatory DNA sequences in a cell of interest, according to the patent’s abstract. The patent also describes “libraries of regulatory sequences obtained according to the methods, and databases comprising collections of regulatory sequences for a particular cell of interest,” according to the abstract.

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