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Recent Patents in Bioinformatics, April — May 2007

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US Patent 7,215,804. Method and apparatus for providing a bioinformatics database. Inventors: David Balaban, Arun Aggarwal. Assignee: Affymetrix.
 
The patent protects a method for organizing information relating to polymer probe array chips, including oligonucleotide array chips. The patent abstract describes a database model that organizes information relating to sample preparation, chip layout, application of samples to chips, scanning of chips, and expression analysis of chip results, etc. The model is “readily translatable” into database languages such as SQL, according to the patent abstract, and scales to permit mass processing of probe array chips.
 

 
US Patent 7,212,951. Method for characterizing and analyzing 3-D shapes of molecules utilizing steric multiplets. Inventors: Edmond Abrahamian, Robert Clark, Peter Fox, Essam Metwally. Assignee: Tripos.
 
The patent abstract describes a method for representing steric features in the three-dimensional disposition of atoms in molecules as “multiplets” using a defined set of steric descriptors. The resulting multiplets can be encoded in bitmaps, which can be generated in compressed form and used to compare individual conformers or ensembles of conformers of molecules to each other without decompression. These comparisons are useful in molecular similarity analysis, in molecular diversity analysis, in database searching, and in conformational analysis, the abstract states.
 

 
US Patent 7,212,924. Method of inferring three-dimensional structure of protein. Inventor: Akiko Itai. Assignee: None.
 
The patent abstract describes a method of predicting a scaffold of a protein based on a query sequence. The method uses a database containing information on the side chain of each amino acid residue contained in the sequence of each reference protein whose three-dimensional structure is known. The method chooses at least one template protein among the reference proteins that has high similarity in three-dimensional structure to the protein comprising the query sequence, and predicts the scaffold of the protein comprising the query sequence.
 

 
US Patent 7,211,388. Method for profiling and identifying persons by using data samples. Inventors: Howard Cash, Simon Mercer, Jonathon Hoyle, Lucy Hadden, Amy Sutton, David Relyea, William Wake, Matthew Smith, Tom Kubit, Greg Poth, Anna Korn, Anna Khizhnyak, Tracy Beeson. Assignee: Gene Codes Forensics.
 

The patent abstract describes a method for profiling and identifying persons by using data samples. The method uses a list of one or more aggregated matching samples with consistent STR profiles. A method for aggregating samples from a plurality of disparate samples, and combining the aggregated samples is also provided.

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The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.