Base sequence cluster generating system, base sequence cluster generating method, program for performing cluster generating method, and computer readable recording medium on which program is recorded and system for providing base sequence Information
AssigneeInternational Business Machines Corporation
InventorTetsuo Shibuya
Life of this patent
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Abstract
A base sequence cluster generating system, method, and program product for performing cluster generation,. This is accomplished utilizing a computer system having a database containing base sequences receives a query sequence over. The computer uses spliced base sequences as a query sequence to generate a first cluster including base sequences that are likely to constitute a spliced pair with the query sequence. Spliced alignment is applied to the generated first cluster to generate a second cluster including spliced pairs. The generated second cluster is returned to the requester.
Claims16
1) A system for generating a cluster of base sequences with respect to splicing, said system generating spliced base sequences from a base sequence, said system comprising:
- a subsystem for recording said spliced base sequences as a query sequence;
- a subsystem for comparing a spliced edit distance between said query sequence and said base sequence read from a database with a predetermined maximum acceptable value;
- and
- a subsystem for selecting spliced base sequences of which the spliced edit distance between said query sequence and said base sequence is not more than said maximum acceptable value to generate a first cluster and recording said first cluster in a storage subsystem.
7) A method for generating a cluster of base sequences with respect to splicing, said splicing generates spliced base sequences from a base sequence, wherein said method comprises the steps of:
- recording said spliced base sequences as a query sequence;
- comparing a spliced edit distance between said query sequence and said base sequence read from a database with a predetermined maximum acceptable value;
- and
- selecting spliced base sequences of which the spliced edit distance between said query sequence and said base sequence is not more than said maximum acceptable value to generate a first cluster and recording said first cluster in storage.
11) A computer-readable recording medium on which a program is recorded, said program causing a computer system to perform a method for generating a cluster of base sequences with respect to splicing, said splicing generating spliced base sequences from a base sequence, said program causing said computer system to perform the steps of:
- recording said spliced base sequences as a query sequence;
- comparing a spliced edit distance between said query sequence and said base sequence read from a database with a predetermined maximum acceptable value;
- and
- selecting spliced base sequences of which the spliced edit distance between said query sequence and said base sequence is not more than said maximum acceptable value to generate a first cluster and recording said first cluster in storage means.
14) A base sequence information processing system for providing information about a cluster of base sequences with respect to splicing, said splicing generating spliced base sequences from a base sequence, said system comprising:
- a server for receiving a query sequence;
- and
- a database containing base sequences;
- wherein said server comprises:
- a subsystem for recording said spliced base sequences as a query sequence;
- a subsystem for comparing a spliced edit distance between said query sequence and said base sequence read from a database with a predetermined maximum acceptable value;
- a subsystem for selecting spliced base sequences of which the spliced edit distance between said query sequence and said base sequence is not more than
- said maximum acceptable value to generate a first cluster and recording said first cluster in storage a subsystem;
- a subsystem for generating a second cluster from said first cluster and storing said second cluster in storage;
- and
- a subsystem for sending said second cluster over said network.
Dependencies are inferred from the claim text.