US Patent 6,636,849. Data search employing metric spaces, multigrid indexes, and B-grid trees. Inventors: Yuanhua Tang, Yonghong Yang. Assignee: GenMetrics.
Protects systems and methods for fast searching for homologous matches in a large quantity of data in metric space. Applications include homology searching for DNA and/or protein sequences, textual or byte-based searches, or literature searching based on lists of keywords. The invention can be used in combination with existing sequence comparison algorithms, such as Fasta and Blast.
US Patent 6,633,819. Gene discovery through comparisons of networks of structural and functional relationships among known genes and proteins. Inventors: Andrey Rzhetsky, Sergey Kalachikov. Assignee: The Trustees of Columbia University in the City of New York.
Covers methods for identifying novel genes using databases containing information on gene/protein structure, function, and/or regulatory interactions. The system detects sequence similarities and domain/motif matches between genes/proteins; computes and interprets phylogenetic trees for multigene families; and analyzes homologous regulatory networks to detect novel genes.
US Patent 6,633,817. Sequence database search with sequence search trees. Inventors: Michael Walker, James Wang, Eldar Giladi. Assignee: Incyte Genomics (now Incyte Corp.)
Protects a method and system for generating and searching a tree-structured index of window vectors that represent database sequences. The system comprises a window vector generation module, which partitions a database sequence into a plurality of overlapping windows with a fixed length comprising a fixed number of nucleotides; a tree-structured index generation module; a query sequence partitioning module; and a retrieval component.
US Patent 6,631,332. Methods for using functional site descriptors and predicting protein function. Inventors: Jeffrey Skolnick; Jacquelyn Fetrow. Assignee: The Scripps Research Institute.
Protects methods and systems for predicting the biological functions of proteins based on functional site descriptors for discrete protein biological functions. Functional site descriptors are geometric representations of protein functional sites in three-dimensional space, and can also include additional parameters, such as conformational information. In preferred embodiments, a library of functional site descriptors is used to probe inexact protein structures derived by computational methods from amino acid sequence information to predict biological function.
US Patent 6,631,331. Database system for predictive cellular bioinformatics. Inventors: James Sabry, Cynthia Adams, Eugeni Vaisberg, Anne Crompton. Assignee: Cytokinetics.
Covers a system for acquiring knowledge from cellular information that is based on a database management module (DBMS). The system also has a population module coupled to the DBMS for categorizing and storing features (such as cell size, distance between cells, cell population, or cell type) from an image acquisition device. A prediction module is coupled to the DBMS.
US Patent 6,631,211. Interactive system for analyzing scatter plots. Inventors: Mack Schermer; Todd Stephan. Assignee: PerkinElmer.
Covers a system for analyzing differential gene expression data. A scanner system analyzes data plotted in accordance with user-specified differential expression ratios or statistical measures to produce a scatter plot that displays the boundaries for the selection of outlier points or otherwise visually denotes which points are the outlier points. Alternatively, the system may analyze the underlying data based on absolute expression levels.
US Patent 6,625,585. Method and system for artificial intelligence directed lead discovery though multi-domain agglomerative clustering. Inventors: John MacCuish; Christodoulos Nicolaou. Assignee: Bioreason.
Protects a system for identifying pharmacophoric mechanisms based on a set of input data that represents many chemical compounds. Given an input data set defining, for each compound, a feature characteristic and an activity characteristic, a computer agglomeratively clusters representations of the molecules based on their feature characteristics.
US Patent 6,625,545. Method and apparatus for mRNA assembly. Inventors: Mor Amitai; Raveh Gill-More; Eran Halperin; Avner Magen; Sarah Pollock. Assignee: Compugen.
Covers a method for the automatic assembly of mRNA sequences from databases containing large numbers of partial cDNA sequences. The method obtains an mRNA sequence having alternative spliced variants from a database of ESTs.