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Recent Patents in Bioinformatics, September 2005

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US Patent 6,941,317. Graphical user interface for display and analysis of biological sequence data. Inventors: Stephen Chamberlin, Steven Benner, Lukas Knecht. Assignee: Eragen Biosciences.

Protects a computer research tool that searches data from various databases and provides a graphical user interface that enhances biological data representation, progressive querying, and cross-navigation of windows and databases. The invention can be implemented in numerous ways, including as a system, a device, a method, or a computer readable medium, according to the patent abstract.


US Patent 6,934,636. Methods of genetic cluster analysis and uses thereof. Inventors: Boguslaw Skierczynski, Nicholas Schork. Assignee: Genset.

Covers methods of genetic cluster analysis for use in determining the homogeneity and/or heterogeneity of a population or sub-population.


US Patent 6,931,401. Methods and apparatus for high-speed approximate sub-string searches. Inventors: Michael Gibson, Richard Messenger, Marc Rieffel, Zheng Zhang. Assignee: Paracel.

Covers a method and system for conducting sequence searches in a sequence database. In one embodiment, the method combines a plurality of query sequences into a combined query sequence; determines a plurality of subdivisions of the sequence database; performs a plurality of searches, wherein each search includes a comparison of the combined query sequence against one of the plurality of subdivisions of the database to produce a plurality of word matches; extends the length of the plurality of word matches to produce a plurality of high-scoring segment pairs; and produces a plurality of reports, each report representing the highest scoring matches for one of the plurality of query sequences.


US Patent 6,931,396. Biological data processing. Inventors: Thodoros Topaloglou, Anthony Kosky. Assignee: Gene Logic.

Protects a multi-database query system that queries a plurality of databases and servers, including an input that receives queries in a structured form and a translation server that translates at least a part of a received query into commands recognized by a data manipulation server.


US Patent 6,931,326. Methods for obtaining and using haplotype data. Inventors: Richard Judson, Claiborne Stephens, Andreas Windemuth. Assignee: Genaissance Pharmaceuticals.

Protects methods, computer programs, and databases to analyze and make use of gene haplotype information. These include methods, program, and a database to find and measure the frequency of haplotypes in the general population; methods, program, and a database to find correlations between an individual's haplotypes or genotypes and a clinical outcome; methods, program, and a database to predict an individual's haplotypes from the individual's genotype for a gene; and methods, program, and a database to predict an individual's clinical response to a treatment based on the individual's genotype or haplotype.


US Patent 6,928,368. Gene mining system and method. Inventors: Lee Bulla Jr., Mehmet Candas. Assignee: The Board of Regents, The University of Texas System.

Covers a computer-based system, method and apparatus for targeting gene sequences having one or more phenotypic characteristics. One or more phenotypic characteristics are selected. A gene sequence is then selected that is known to have the selected phenotypic characteristics. In addition, one or more databases containing cataloged gene sequences are selected. The selected gene sequence is compared to the cataloged gene sequences, and any cataloged gene sequences that contain a portion of the selected gene sequence are extracted. The selected gene sequence is aligned to each portion of the extracted gene sequence and the extracted gene sequences are prioritized based on the alignment of the selected gene sequence. At least one of the prioritized gene sequences is selected based on one or more phenotypic criteria. Finally, one or more degenerate primers are designed to target the selected-prioritized gene sequences.


US Patent 6,925,389. Process for discriminating between biological states based on hidden patterns from biological data. Inventors: Ben Hitt, Emanuel Petricoin, Peter Levine, Lance Liotta. Assignee: Correlogic Systems, The United States of America as Represented by the Department of Health and Human Services.

Protects a process for determining a biological state through the discovery and analysis of hidden or non-obvious discriminatory biological data patterns. The biological data can be from health data, clinical data, or from a biological sample that is analyzed to determine the biological state of the donor.

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The Scan

Guidelines for Ancient DNA Work

More than two dozen researchers have developed new ethical guidelines for conducting ancient DNA research, which they present in Nature.

And Cleared

A UK regulator has cleared former UK Prime Minister David Cameron in concerns he should have registered as a consultant-lobbyist for his work with Illumina, according to the Financial Times.

Suit Over Allegations

The Boston Globe reports that David Sabatini, who was placed on leave from MIT after allegations of sexual harassment, is suing his accuser, the Whitehead Institute, and the institute's director.

Nature Papers on Esophageal Cancer, Origin of Modern Horses, Exome Sequencing of UK Biobank Participants

In Nature this week: genetic and environmental influences of esophageal cancer, domestic horse origin traced to Western Eurasian steppes, and more.