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Recent Patents in Bioinformatics

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US Patent 6,922,638. System and method for transacting and manipulating a multi-sequence search using biological data repositories. Inventors: James Wallace, Kai Wang, John Liljeberg. Assignee: PhenoGenomics.

Covers a system and method for transacting and manipulating a multi-sequence search using a biological data repository. According to the patent abstract, a set of search query parameters specifying a plurality of sequence sets, in which each sequence set encodes structured biological data values, is received. A search queue is loaded with the search query parameters formatted into a structured database query for each sequence set assigned by search type. A search of the biological data repository is launched for each sequence set, and search results are retrieved. The search results are received as sequence set information organized and reformatted for each sequence set and search type. A plurality of sequences are aligned using the search results based on one or more structured biological data values having matching characteristics. The aligned sequences are forwarded with matching characteristics indicators.


US Patent 6,920,448. Domain specific knowledge-based metasearch system and methods of using. Inventors: Robert Kincaid, Simon Handley; Aditya Vailaya, Parvathi Chundi. Assignee: Agilent Technologies.

Protects a system and method for performing domain-specific knowledge-based metasearches. According to the patent abstract, the method comprises a metasearch engine for accessing and searching text-based documents using generic search engines while simultaneously being able to access publication-based databases and sequence databases as well as in-house proprietary databases and any database capable of being interfaced with a web interface so as to produce search results in text format. A data-mining module is also provided for organizing raw data obtained by unsupervised clustering, simple relevance ranking, and categorization, all of which are done independently of one another. According to the inventors, the method can be used to search standard web-based sites that are accessible by search engines such as Google and Altavista, as well as sites such as PubMed, GenBank, OMIM, sequence databases, protein structure databases such as PDB, pathway information databases, and other data-specific sites.


US Patent 6,920,398. Haplotype determination. Inventors: Jun Liu, Zhaohui Qin, Tianhua Niu. Assignee: President and Fellows of Harvard College.

Protects a method for determining haplotypes for phased genotypic information from unphased genotypic information. One method includes separating a dataset that includes genotypic information for a plurality of markers for each of a plurality of individuals into subdatasets, each subdataset including the genotypic information for a subset of the markers; for each subdataset, identifying haplotypes compatible with marker information for each marker of the subset and for each individual; and for each individual, assembling the haplotypes from each of the subsets to provide the individual's haplotype with respect to the markers.


US Patent 6,920,397. Repeatable software-based active signal processing technique. Inventor: Sandeep Gulati. Assignee: ViaLogy.

Covers a technique for determining the presence of specific hybridization expression within an output pattern generated from a digitized image of a biological sample applied to an arrayed platform. The output pattern includes signals associated with noise, and signals associated with the biological sample, some of which are degraded or obscured by noise. The output pattern is first segmented using tessellation. Signal processing, such as interferometry is then used to amplify signals associated with the biological sample within the segmented output pattern having an intensity lower than the intensity of signals associated with noise so that they may be clearly distinguished from background noise.


US Patent 6,920,396. System and method for providing flexible access and retrieval of sequence data from a plurality of biological data repositories. Inventors: James Wallace, Kai Wang, John Liljeberg. Assignee: PhenoGenomics.

Covers a system and method for retrieving sequence data from several biological data repositories. Each data repository contains sequence data stored into structured records that are uniquely identified. Each data repository is interfaced through a queue handler dynamically locating and selecting at least one such biological data repository and launching a search query against each selected biological data repository. Search query parameters are accepted from a user specifying a search request for a sequence set. Results obtained from a search engine are presented as ordered tables of search results.


US Patent 6,917,883. Efficient cis-element discovery method using multiple sequence comparisons based on evolutionary relationships. Inventors: Frank Ruddle, Kenta Sumiyama, Chang-Bae Kim. Assignee: Yale University.

Protects a method for efficiently searching non-coding DNA for known control elements. According to the patent abstract, short conserved DNA sequences can be identified among three or more species by selecting DNA sequences from species having a total genetic distance larger than one substitution per site at a neutrally evolving region and calculating the total substitutions using pairwise genetic distances, with the pairs for comparison selected based on phylogenetic relationships.


US Patent 6,917,882. Methods for making character strings, polynucleotides and polypeptides having desired characteristics. Inventors: Sergey Selifonov, Willem Stemmer, Claes Gustafsson, Matthew Tobin, Stephen del Cardayre, Phillip Patten, Jeremy Minshull. Assignee: Maxygen.

Protects methods for in silico nucleic acid recombination and related integrated systems using genetic operators and libraries made by in silico DNA-shuffling methods. According to the patent abstract, part or all of the DNA-shuffling procedure is performed or modeled in a computer system, "avoiding (partly or entirely) the need for physical manipulation of nucleic acids." These approaches are collectively termed Genetic Algorithm Guided Gene Synthesis (GAGGS).

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The Scan

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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.