Methods for establishing a pathways database and performing pathway searches
First Claim
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1. A computerized storage and retrieval system of biological information comprising:
- a means for data entry;
a means for displaying the data;
a programmable central processing unit for performing automated analysis; and
a data storage means containing protein pathways and annotated information on the pathways stored in a relational database, wherein the pathways annotated and organized in a curated clustering arrangement and wherein the annotated information is accessed through the relational database.
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Abstract
The invention provides a computerized storage and retrieval system for storing biological information organized as a protein pathways database and methods for performing pathway searches on nodes (proteins or other molecules), modes (interactions), and nodes-and-modes. The protein pathways database is a relational database that integrates protein sequence, genomic sequence, gene-expression, protein interactions, protein-protein association and pathway data and can be searched using a query pathway to predict homologous or orthologous nodes, modes, and pathways.
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Citations
22 Claims
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1. A computerized storage and retrieval system of biological information comprising:
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a means for data entry;
a means for displaying the data;
a programmable central processing unit for performing automated analysis; and
a data storage means containing protein pathways and annotated information on the pathways stored in a relational database, wherein the pathways annotated and organized in a curated clustering arrangement and wherein the annotated information is accessed through the relational database. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22)
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16. A method of using a known protein pathway to predict the nodes and modes of a novel pathway comprising:
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a) submitting a query pathway and known protein sequences;
b) applying standard methods of comparison to determine similarity between the known protein sequences and protein sequences in the protein databases, thereby predicting candidate nodes;
c) utilizing coefficients of similarity from protein interactions or protein-protein association data, thereby predicting candidate modes; and
d) retrieving novel pathways with an OP-score obtained using an optimization algorithm. - View Dependent Claims (17, 18)
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19. A method for predicting novel pathways comprising:
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a) generating candidate proteins from one species for each node based on a protein search;
b) employing a means for optimization to find likely linear linkages between candidate proteins aligned to the query pathway with possible gaps in the alignment, and c) reporting all pathways with optimal and sub-optimal predictions that satisfy user-specified alignment and interaction parameters wherein the accuracy of the prediction is provided by OP-score. - View Dependent Claims (20)
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Specification