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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Jun 9, 2003


US Patent 6,571,230. Methods and apparatus for performing pattern discovery and generation with respect to data sequences. Inventor: Laxmi Parida. Assignee: International Business Machines.

Describes a method for detecting repeating patterns in an input data sequence. The invention provides that, for any sequence, there exists only a linear number of special motifs and every other motif can be generated from these so-called “irredundant” motifs.


US Patent 6,571,227. Method, system and computer program product for non-linear mapping of multi-dimensional data. Inventors: Dimitris Agrafiotis, Victor Lobanov, Francis Salemme. Assignee: 3-Dimensional Pharmaceuticals.

Covers a scalable computer system for dimensionally reducing multi-dimensional data sets. The method determines one or more non-linear functions between a sample of points from the multi-dimensional data set and a corresponding set of dimensionally reduced points, and then uses the non-linear function to non-linearly map additional points.


US Patent 6,571,199. Method and apparatus for performing pattern dictionary formation for use in sequence homology detection. Inventors: Aris Floratos, Isidore Rigoutsos. Assignee: International Business Machines.

Covers a computer-based method of processing a plurality of sequences in a database. The method first evaluates each of the plurality of sequences, including characters that form each sequence. Then, at least one pattern of characters is generated representing at least a subset of the sequences in the database. The statistical significance of the pattern is then determined by a value representing a minimum number of sequences that the pattern supports in the database.


US Patent 6,567,540. Method and apparatus for providing a bioinformatics database. Inventors: David Balaban, Arun Aggarwal. Assignee: Affymetrix.

Protects a system and method for organizing information relating to polymer probe array chips, including oligonucleotide array chips, using a database model to organize information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, expression analysis of chip results, etc.


US Patent 6,564,151. Assigning protein functions by comparative genome analysis of protein phylogenetic profiles. Inventors: Matteo Pellegrini, Edward Marcotte, Michael Thompson, David Eisenberg, Robert Grothe, Todd Yeates. Assignee: The Regents of the University of California.

Describes computational systems 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 that can be revealed by a trans-genome comparison. 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.


US Patent 6,560,542. 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: the Cielo Institute.

Protects algorithms for designing peptides or peptide analog molecules capable of binding to and/or modulating the function of protein targets having known amino acid sequences. The methods use three kinds of templates to produce the peptides.

Filed under

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.