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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Sep 2, 2002


US Patent 6,438,496. Method and apparatus for revealing latent characteristics existing in symbolic sequences. Inventors: Tetsuhiko Yoshida, Kenji Oosawa, Nobuaki Obata. Assignee: Toa Gosei.

Protects a method for expressing “a characteristic or regularity“ existing in a symbolic sequence that begins with a known single symbolic sequence, such as a nucleotide sequence of DNA or an amino acid sequence of protein, that is broken down into smaller non-overlapping portions and then placed in parallel to reveal previously unrecognized characteristics in the entire sequence.


US Patent 6,434,488. Alignment-free methodology for rapid determination of differences between a test data set and known data sets. Inventor: Barry Robson. Assignee: International Business Machines.

Provides methods and apparatus for performing alignment-free determination of differences between a test data set and known data sets. The patent describes a method for generating data characterizing an item described by an ordered string of characters, such as a protein sequence in which each character in the ordered string of characters represents an amino acid.


US Patent: 6,432,361. Method and apparatus for identifying, classifying, or quantifying protein sequences in a sample without sequencing. Inventors: Jonathan Rothberg, Michael Deem, John Simpson. Assignee: CuraGen.

Protects methods by which biologically derived DNA sequences in a mixed sample or in an arrayed single sequence clone can be determined and classified without sequencing. An embodiment of the invention uses information on the presence or absence of carefully chosen target subsequences in a single sequence clone together with DNA sequence databases to determine the clone sequence. Computer-implemented methods analyze the experimental results and determine the sample sequences in question. US Patent 6,418,382, also assigned to CuraGen, covers a similar method for quantifying DNA sequences.


US Patent 6,424,921. Averaging multiple hybridization arrays. Inventors: Robert Gupta, Kirindi Choi, Robert Brahms, Doris Chang, Darryl Chong, John Burrill, Gregory Marcus; Gabor Bartha, Richard Head. Assignee: Incyte Genomics.

Covers a computer-implemented method of averaging several hybridization data arrays. Composite hybridization arrays are formed from a user-selected set of hybridization arrays, instantiated in a hybridization array database, and made available for searching, analysis, and other data processing.


US Patent 6,421,613. Data processing of the maize prolifera genetic sequence. Inventors: Ramgopal Nadimpalli, Carl Simmons. Assignee: Pioneer Hi-Bred International.

Covers a data processing system for isolated prolifera nucleic acids and their encoded proteins.


US Patent 6,420,108. Computer-aided display for comparative gene expression. Inventors: David Mack, Elina Khurgin, Josie Dai, Kurt Gish, Jim Snyder, David Balaban. Assignee: Affymetrix.

Protects systems and methods for visualizing information collected from analyzing samples, including nucleic acids, proteins, or other polymers. In one embodiment, a computer system displays the expression levels of multiple genes simultaneously in a way that facilitates user identification of genes. Additionally, the computer system may facilitate display of further information about relevant genes once they are identified.


US Patent 6,410,239. Identification and comparison of protein-protein interactions that occur in populations and identification of inhibitors of these interactors. Inventors: Krishnan Nandabalan, Jonathan Rothberg, Meijia Yang, James Robert Knight; Theodore Samuel Kalbfleisch, Assignee: CuraGen.

Protects methods for detecting protein-protein interactions among two populations of proteins using two yeast strains. Also covers information-processing methods and systems to identify the genes coding for detected interacting proteins, assemble a unified database of protein-protein interaction data, and process this unified database to obtain protein interaction domain and protein pathway information.


US Patent 6,408,308. System and method for generating, analyzing and storing normalized expression datasets from raw expression datasets derived from microarray includes nucleic acid probe sequences. Inventors: Timothy Maslyn, Srikar Rao, Benjamin Cocks, Rachel Cheng, Timothy Engler, James Kerr, Steven Lassagne, Jeffrey Seilhamer. Assignee: Incyte.

Protects a biomolecular expression information processing system with procedures and tables that store abundance datasets and hybridization data. The tables also store information identifying a microarray technology type for each hybridization and microarray design information for each microarray technology type.

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