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

• US 9,589,102 B2
• Filed: 08/12/2011
• Issued: 03/07/2017
• Est. Priority Date: 05/21/2002
• Status: Expired due to Fees

• Current Assignee: International Business Machines Corporation
• Original Assignee: International Business Machines Corporation
• Inventors: Shibuya, Tetsuo
• Primary Examiner(s): NEGIN, RUSSELL SCOTT
• Application Number:
  US13/209,097
• Publication Number:
  US 20110295977A1
• Time in Patent Office: 2,034 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 5/00 ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks

Abstract

Provided is a base sequence cluster generating system, method, and program product for performing cluster generation. The base sequence cluster generating system utilizes 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.

Claims

1. A system for providing information about a cluster of child spliced sequences obtained from a parent base sequence comprising a server for receiving a query sequence and a database containing base sequences, wherein said server comprises:

a subsystem for recording a plurality of spliced sequences, wherein each spliced sequence is a query sequence;

a subsystem for comparing a spliced edit distance between each query sequence and the parent 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 each query sequence and the parent base sequence is not more than said maximum acceptable value to generate a first cluster of child spliced sequences and recording said first cluster in a storage subsystem;

a subsystem for generating a second cluster of child spliced sequences from said first cluster and storing said second cluster; and

a subsystem for sending said second cluster over a network, wherein the second cluster of child spliced sequences comprises spliced pairs between each query sequence and the base sequence with a defined splice length for the base sequence and applying spliced alignment between each query sequence and the first cluster as aligned with the base sequence, wherein the degree of spliced alignment between each query sequence and the base sequence is determined by the number of spliced pairs of the second cluster at the defined splice length.

2. The system of claim 1, wherein said spliced edit distance comparing subsystem comprises a difference counter decrementing from said maximum acceptable value when a base in said base sequence matches a base in each query sequence.

3. The system of claim 1, wherein said network is Internet based.

4. The system of claim 1, wherein said network is a local area network (LAN).

5. The system of claim 3, further comprising:

a subsystem for assigning a score to the base sequence based upon the degree of spliced alignment between the query sequence and the base sequence as determined by the number of spliced pairs of the second cluster;

a subsystem for generating a table by repeated generation of said score to correspond to the splice length; and

a subsystem for using contents of said table to determine a score for said base sequence with respect to each query sequence.

6. The system of claim 1, wherein said splice length is the number of bases within the range from 20 to 60.

7. The system of claim 1, wherein said parent base sequence from the database comprises a DNA sequence of a eukaryote.

8. The system of claim 1, wherein said query sequence comprises DNA spliced sequences.

9. The system of claim 1, wherein said query sequence comprises cDNA spliced sequences obtained through reverse transcription from mRNA expressed in said eukaryote.

10. The system of claim 1, wherein said query sequence comprises cDNA spliced sequences obtained through reverse transcription from mRNA expressed in base sequences of said mRNA.

11. The system of claim 1, wherein said second cluster is stored in computer memory.

12. The system of claim 1, wherein said second cluster is stored in a computer hard disk.

13. The system of claim 1, wherein said stored second cluster is displayed on a display screen.

14. The system of claim 1, wherein said server is connected to the network and said query sequence is received by said server over said network.

15. The system of claim 14, wherein said network is Internet based.

16. The system of claim 14, wherein said network is a local area network (LAN).

17. The system of claim 14, wherein said server further comprises communication means for communicating with clients over the network.

18. The system of claim 17, wherein said communications means are selected from the group consisting of a network interface card (NIC), a modem, and a data service unit (DSU).

19. The system of claim 17, wherein said clients are connected to the server over the network with a medium selected from the group consisting of an Ethernet®

connection, a public telephone line, an integrated service digital network (ISDN), an optical communication line, and an asymmetric digital subscriber line (ADSL).