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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Sep 20, 2004

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US Patent 6,792,356. Apparatus and method for automated protein design. Inventors: Stephen Mayo, Bassil Dahiyat, Benjamin Gordon, Arthur Street. Assignee: California Institute of Technology.

Covers computer-implemented methods for quantitative protein design and optimization. The method first receives a protein backbone structure with variable residue positions, and establishes a group of potential rotamers for each of the variable residue positions. The method then analyzes the interaction of each of the rotamers with all or part of the remainder of the protein backbone structure to generate a set of optimized protein sequences.


US Patent 6,792,355. Methods for determining polypeptide structure, function or pharmacophore from comparison of polypeptide sequences. Inventors: Mark Hansen, Richard Kho, Hugo Villar. Assignee: Triad Therapeutics.

Describes a method for separating subsets of polypeptides. The method first determines a sequence comparison signature for each amino acid sequence in a set of amino acid sequences. This signature includes pairwise comparison scores for each sequence compared to each of the other sequences in the set. The method then constructs a distance arrangement by relating the distance between each of the signatures and identifies clusters of sequence comparison signatures in the distance arrangement.


US Patent 6,789,069. Method for enhancing knowledge discovered from biological data using a learning machine. Inventors: Stephen Barnhill, Isabelle Guyon, Jason Weston. Assignee: BIOwulf Technologies.

Covers a learning machine, such as a support vector machine, that is used to extract information from large quantities of biological data. The method includes pre-processing of training data and test data to add dimensionality or to identify missing or erroneous data points. After the training has been confirmed, live biological data can be pre-processed and then input into the trained learning machine for extraction of useful information.


US Patent 6,789,020. Expert system for analysis of DNA sequencing electropherograms. Inventors: Arthur Miller, Barry Karger. Assignee: Northeastern University.

Protects a method for analyzing DNA fragments separated electrophoretically. The method uses an expert system that interprets raw or preprocessed signal from the separation. The system can be used for real-time base-calling, or applied offline after data acquisition.


US Patent 6,785,672. Methods and apparatus for performing sequence homology detection. Inventors: Aris Floratos, Isadore Rigoutsos. Assignee: International Business Machines.

Protects a computer-based method of detecting homologies between sequences in a database and a query sequence. First, the method accesses patterns associated with the database, each pattern representing at least a portion of one or more sequences in the database. Next, the query sequence is compared to the patterns to detect whether one or more portions of the query sequence are homologous to portions of the sequences of the database represented by the patterns. A score is generated for each sequence detected to be homologous to the query sequence.


US Patent 6,775,622. Method and system for detecting near identities in large DNA databases. Inventor: James Holloway. Assignee: ZymoGenetics.

Protects a system and method for efficiently detecting near-identities in large DNA databases based on an algorithm used to construct a DNA database in which no two DNA sequences is nearly identical to a region of the other. According to the inventors, the system and method are applicable to problems such as an all-against-all comparison of all the DNA sequences in a DNA database and other bioinformatics tasks.


US Patent 6,772,160. Techniques for facilitating information acquisition and storage. Inventors: Raymond Cho, Richard Chen, Ramon Felciano, Daniel Richards, Philippa Norman. Assignee: Ingenuity Systems.

Protects a method and system for extracting information from a plurality of articles and for storing the extracted information in a knowledge-based information store. The method identifies articles and assigns information extractors for extracting information from those articles. A content reviewer reviews the extracted information received from the information extractor and identifies errors associated with the extracted information.


US Patent 6,772,069. Determining protein function and interaction from genome analysis. Inventors: David Eisenberg, Edward Marcotte, Michael Thompson, Matteo Pellegrini, Todd Yeates. Assignee: University of California, Los Angeles.

Describes a computational system and computer program for inferring functional links from genome sequences. One method is based on the observation that some pairs of proteins have homologs in another organism fused into a single protein chain. Another method compares the genomic sequence of two or more organisms to create a phylogenetic profile for each protein indicating its presence or absence across all the genomes. In yet another method a combination of the above two methods is used to predict functional links.


US Patent 6,768,982. Method and system for creating and using knowledge patterns. Inventors: Mark Collins, John Shaw, Ricard Colasanti. Assignee: Cellomics.

Protects a method for acquiring one or more patterns from one or more pharmaceutical data sources. A knowledge map is created using these patterns that includes a selected representation of a pattern space. According to the inventors, the knowledge map is used for recognizing previously unseen or unknown patterns from large amounts of pharmaceutical data obtained by automated screening systems.


US Patent 6,763,308. Statistical outlier detection for gene expression microarray data. Inventors: Tzu-Ming Chu, Russell Wolfinger. Assignee: SAS Institute.

Covers a computer-implemented method and system for detecting outliers in microarray data. A mixed linear statistical model is used to generate predictions based upon the received microarray data. Residuals are generated by subtracting model-based predictions from the original microarray sample data. Statistical tests are performed for residuals by adding covariates to the mixed model and testing their significance.

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