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BioInform s IP Roundup: Recent Patents in Bioinformatics: Jun 6, 2005

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US Patent 6,898,531. Algorithms for selection of primer pairs. Inventors: John Sheehan, Daryl Thomas, Wade Barrett. Assignee: Perlegen Sciences.

Covers methods for amplifying a DNA target sequence. In a first aspect of the invention, a method for designing primer pairs for the amplification reaction is provided. The patent also protects computer-implemented methods for carrying out the claims of the invention.


US Patent 6,898,530. Method and apparatus for extracting attributes from sequence strings and biopolymer material. Inventors: Jeffrey Saffer, Augustin Calapristi, Nancy Miller, Randall Scarberry, Heidi Sofia, Lisa Stillwell, Guang Chen, Philip Monroe. Assignee: Battelle Memorial Institute.

Protects systems for creating high-dimensional vectors representing sequence strings and biopolymer materials. A first system divides respective sequence strings into blocks of at least three units to create a vocabulary of blocks; a second system selects predefined domains of a plurality of items of biopolymer materials; a third system defines each item of biopolymer material in a data set of biopolymer materials as a surface using descriptors of at least one of structure and function; and a fourth system compares information regarding each biopolymer material to information regarding other biopolymer materials.


US Patent 6,897,875. Methods and system for analysis and visualization of multidimensional data. Inventor: Ji Zhang. Assignee: The Board of the University of Nebraska.

Covers methods for facilitating pattern recognition in complex biological data using component plane presentations of clustered data.


US Patent 6,895,396. Neural network methods to predict enzyme inhibitor or receptor ligand potency. Inventors: Steven Schwartz, Vern Schramm, Benjamin Braunheim. Assignee: Albert Einstein College of Medicine of Yeshiva University.

Protects a method for predicting the binding energy for enzyme-transition state inhibitor interactions using computational neural networks that analyze the quantum mechanical features of transition states and the putative inhibitors necessary for binding. According to the inventors, experimental results show that the neural networks can predict with quantitative accuracy the binding strength of new inhibitors. The method is also applicable to predicting the binding free energy of a ligand to a receptor, which would permit evaluation of chemical libraries of potential inhibitory, agonistic, or antagonistic agents.


US Patent 6,895,340. Method of molecular structure recognition. Inventors: Feng Xu, Steven Klohr, David Detlefsen. Assignee: Bristol-Myers Squibb.

Protects an analytical method and apparatus that based on principal component analysis of nuclear magnetic resonance data for rapid molecular structure/function pattern recognition. The presence of a molecular substructure in an organic compound is determined by comparing principal components calculated from chemical shift values of the substructure in selected compounds with those calculated from the chemical shift values of the organic compound.


US Patent 6,895,337. Method of identifying genomic rearrangements. Inventors: Thomas Scholl, Dmitry Pruss, Brant Hendrickson. Assignee: Myriad Genetics.

Protects a computer program and system for detecting large genomic rearrangements based on unphased genotype data obtained using common genotyping techniques that do not differentiate different alleles. In the method, unphased genotypes at a plurality of nucleotide variant markers of a particular gene in a diploid subject are compared with a canonical haplotype collection of the gene for a heterogeneous subject population. If the unphased genotypes cannot be reduced to a pair of canonical haplotypes within the canonical haplotype collection, it would indicate an increased likelihood that an allele of the gene in the diploid subject harbors a genomic rearrangement, according to the inventors.


US Patent 6,892,141. Primer design system. Inventors: Hiroki Nakae, Sigeo Ihara. Assignee: Hitachi.

Covers a primer-design system in which DNA nucleotide sequences are obtained from a database containing different DNA nucleotide sequences. The method provides a means for predicting the exons of a selected DNA nucleotide and for storing positions of the predicted exons, as well as a means for designing primer pairs by using each of the predicted exons as a template to design a corresponding primer pair for each of the predicted exons. The method also automatically collates the primer pairs with the predicted exons and the DNA nucleotide sequence.


US Patent 6,892,139. Determining the functions and interactions of proteins by comparative analysis. Inventors: David Eisenberg, Sergio Rotstein, Edward Marcotte. Assignee: The Regents of the University of California.

Protects algorithms for identifying a nucleic acid or a polypeptide sequence that may be a target for a drug. The characterization is based on algorithms that can identify functional relationships between diverse sets of non-homologous nucleic acid and polypeptide sequences. The invention provides a computer program product, stored on a computer-readable medium, for identifying a nucleic acid or a polypeptide sequence that may be essential for the growth or viability of an organism or that that may be a target for a drug.


US Patent 6,889,143. Methods and systems for estimating the melting temperature (TM) for polynucleotide molecules. Inventors: Mark Behlke, Lingyan Huang, Richard Owczarzy, Joseph Walder. Assignee: Integrated DNA Technologies.

Protects algorithms and methods for predicting the melting temperature of duplex nucleic acids, particularly duplexes of oligonucleotides that may be used as primers or probes in PCR and/or hybridization assays. The invention also relates to methods and systems for designing and selecting oligonucleotide probes and primers having a predicted melting temperature that is optimized for such assays. The algorithms estimate the melting temperature of a nucleic acid duplex under particular salt conditions using formulas that have terms and coefficients that are functions of the particular nucleotide sequence, to estimate the effect of particular salt conditions on the melting temperature.

 

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