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Recent Patents in Bioinformatics, Dec. 2006 — Jan. 2007

US Patent 7,164,991. Specific identifiers of amino-acid base sequences. Inventors: Tetsuro Toyoda, Akiko Itai. Assignee: Institute of Medicinal Molecular Design (Japan).
Protects a method for assigning specific identifiers to amino-acid sequences and base sequences by generating specific identifiers from data “representing connection order of residues in the sequences by using a conversion function, such as collision intractable hash function or universal one-way hash function,” according to the patent abstract.

US Patent 7,162,372. Least-square deconvolution (LSD): a method to resolve DNA mixtures. Inventors: Tse-Wei Wang, Ning Xue, John Birdwell, Mark Rader, John Flaherty.
Protects a method called least-square deconvolution, which uses quantitative allele peak data derived from a sample containing the DNA of more than one contributor to resolve the best-fit genotype profile of each contributor. The method finds the least square fit of the mass ratio coefficients at each locus to come closest to the quantitative allele peak data.

US Patent 7,158,892. Genomic messaging system. Inventors: Barry Robson, Richard Alan Mushlin. Assignee: IBM.
Protects a computer-based method for transferring data that includes a genomic sequence. The method first identifies at least one genomic base in an input data stream, then assigns a base-specific binary code to genomic base, groups the base-specific binary code to form a genomic data stream representative of the genomic sequence, assigns a command binary code to at least one command for selectively processing the genomic data stream, and then integrates the genomic data stream and command binary code to form an output binary data stream.

US Patent 7,158,891. Method and system to build optimal models of 3-dimensional molecular structures. Inventors: Namasivayam Gautham, Krishnan Vengadesan. Assignee: Council of Scientific & Industrial Research (India).
Protects a method to build three-dimensional models of molecular structures that correspond to the lowest value of the potential energy function. The system uses mutually orthogonal Latin squares to search through conformational space to obtain the best conformation.

US Patent 7,158,889. Gene finding using ordered sets. Inventors: Jagir Hussan, Albee Jhoney. Assignee: IBM.
Covers a computer program for identifying “occurrences of a sequence of ordered marker strings in a string” that particularly relates to “finding a gene in a DNA sequence, according to the patent abstract. The method “includes the steps of identifying sub-strings in the string that match the marker string, creating directed links between a sub-string that matches a particular marker string and all the sub-strings that match a subsequent marker string in the ordered sequence of marker strings, and identifying occurrence/s of the sequence in the string by tracing one or more corresponding path/s from each sub-string that matches the first marker string to all sub-strings that match the last marker string by following the directed links.”

US Patent 7,158,888. Determining structures by performing comparisons between molecular replacement results for multiple different biomolecules. Inventors: Duncan McRee; Peter David, Frank von Delft, John Rammelkamp, Enrique Abola. Assignee: Takeda San Diego.
Protects a method for identifying a search model for determining a structure of a target biomolecule, such as a protein, from X-ray diffraction data. The method uses computer-executable logic to perform multiple molecular replacement searches on X-ray diffraction data of the target biomolecule, in which a group of different biomolecule structures are used as search models for multiple molecular replacement searches. The method compares solutions from the multiple molecular replacement searches to produce data from which biomolecule structures can be identified as having “superior structural identity with the target biomolecule as compared to the other biomolecule structures in the group,” according to the patent abstract.

US Patent 7,158,862. Method and system for mining mass spectral data. Inventors: Daniel Liebler, Beau Hansen, Daniel Mason, Sean Davey, Juliet Jones, Thomas McClure. Assignee: The Arizona Board of Regents on Behalf of the University of Arizona.
Protects a computer program for mining mass spectral data to detect chemical-specific features in large databases. The method specifies characteristics of mass spectra to mine, specifies a relationship between the spectral characteristics, searches for portions of the mass spectra that match the spectral characteristics based on the relationship, and assigns scores to the portions of mass spectra to indicate a degree of correlation between the portions of mass spectra and the spectral characteristics.

US Patent 7,155,453. Biotechnology information naming system. Inventor: Robert Kincaid. Assignee: Agilent Technologies.

Protects systems and methods for performing programmatic queries about molecular and biomolecular information. The methods include creating databases of molecular data formatted according to a directory service protocol, forming a query based on a molecular identifier, submitting the query to a name server, performing a lookup in the databases based on the molecular identifier, retrieving a query result from the databases, and returning the query results to the user.

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The Scan

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The Wall Street Journal reports that prosecutors allege that the co-founder of a biotech arranged to have a business associate who threatened to expose him as a fraud killed.

Whirlwind Decade of CRISPR

The New York Times looks back at the 10 years since the University of California, Berkeley's Jennifer Doudna and her colleagues published their CRISPR paper.

PNAS Papers on Blue Cone Monochromacy Structural Variants, HIV-1 Mutant, T-ALL

In PNAS this week: structural variants linked to blue cone monochromacy, HIV-1 variants affecting the matrix protein p17, and more.