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BioInform s Patent Roundup: Recent Patents of Interest in Bioinformatics: Feb 24, 2003


US Patent 6,522,975. Prediction of molecular polar surface area and bioabsorption. Inventors: William Egan, Giorgio Lauri. Assignee: Pharmacopeia.

Covers a computational method for predicting membrane permeability and physiological absorption of molecules. The method is based on a linear equation incorporating counts of nitrogens, oxygens, and related atom clusters in the molecule.

US Patent 6,521,427. Method for the complete chemical synthesis and assembly of genes and genomes. Inventor: Glen Evans. Assignee: Egea Biosciences.

Protects a computer-directed method for assembling the genes and genomes of synthetic artificial organisms in which sets of gene parts and functional elements are first used to construct a virtual polynucleotide in a computer. Computer software is then used to break down the genome sequence into a set of overlapping oligonucleotides of specified length, which are then synthesized using an array type synthesizer and phosphoamidite chemistry.

US Patent 6,519,583. Graphical viewer for biomolecular sequence data. Inventors: Alex Koleszar, Frank Russo, Joe Don Heath, Stephanie Berry, Rachel Wright, Peter Covitz, Yvonne Boldt, Lee Crawford. Assignee: Incyte Pharmaceuticals (Now Incyte).

Covers methods, media, and systems for graphically displaying computer-based biomolecular sequence information, including nucleotide or amino acid sequence information. The patent covers several different formats for graphical depictions.

US Patent 6,510,391. Computer software products for nucleic acid hybridization analysis. Inventor: David Balaban. Assignee: Affymetrix.

Protects methods and computer software for analyzing gene expression data. In one aspect of the invention, computer software products are provided for determining hybridization between nucleic acid probes and a nucleic acid target.

US Patent 6,512,981. Protein fold recognition using sequence-derived predictions. Inventors: David Eisenberg, Daniel Fischer. Assignee: The Regents of the University of California.

Covers a computer-assisted method for assigning an amino acid probe sequence to a known three-dimensional protein structure. The patent describes a method for using the amino acid sequence of a probe plus sequence-derived properties of the probe to make fold assignments. The method includes entering the amino acid sequence of the probe and at least one sequence-derived property for the probe sequence into the computer system; entering a string of structural properties for each member of a library of known 3D structures; executing an alignment algorithm in the computer; determining the statistical significance of each alignment score to determine a best-fit alignment score; and applying the best-fit alignment score to select the corresponding 3D protein structure from the library for output.


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The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.