Claims
- 1. A computer system, comprising:
a relational database having records containing information identifying
(i) initial sequences of polynucleotide inserts of a plurality of clones, and (ii) reagent specifications of a subset of said plurality of clones; and a user interface allowing a user to selectively view information regarding said sequences and reagent specifications.
- 2. The computer system of claim 1, wherein said records are organized into a plurality of tables.
- 3. The computer system of claim 1, wherein the reagent specifications include physical data and ordering information for said subset of clones.
- 4. The computer system of claim 3, wherein said physical data and ordering information for a clone from said subset of clones includes the clone's processing history, availability, and location.
- 5. The computer system of claim 1, wherein said clones are cDNA clones.
- 6. A computer system, comprising:
a relational database having records containing information identifying
(i) initial sequences of polynucleotide inserts of a plurality of clones, (ii) additional sequences of the polynucleotide inserts of a subset of said plurality of clones, and (iii) reagent specifications of said subset of clones; and a user interface allowing a user to selectively view information regarding said sequences and reagent specifications.
- 7. The computer system of claim 6, wherein said records are organized into a plurality of tables.
- 8. The computer system of claim 6, wherein the reagent specifications include physical data and ordering information for said subset of clones.
- 9. The computer system of claim 8, wherein said physical data and ordering information for a clone from said subset of clones includes the clone's processing history, availability, and location.
- 10. The computer system of claim 6, wherein said clones are cDNA clones.
- 11. A method, implemented on a computer system, for accessing information relating to one or more reagent clones, comprising:
providing a relational database having records containing information identifying
(i) initial sequences of polynucleotide inserts of a plurality of clones, and (ii) reagent specifications of a subset of said plurality of clones; entering, in a graphical user interface, a query relating to one or more of said sequences or reagent specifications; determining matches between said query entry and said information; and displaying the results of said determination.
- 12. The method of claim 11, wherein the reagent specifications include physical data and ordering information for said subset of clones.
- 13. The method of claim 12, wherein said physical data and ordering information for a clone from said subset of clones includes the clone's processing history, availability, and location.
- 14. The method of claim 11, wherein said clones are cDNA clones.
- 15. A method, implemented on a computer system, for accessing information relating to one or more reagent clones, comprising:
providing a relational database having records containing information identifying
(i) initial sequences of polynucleotide inserts of a plurality of clones, (ii) additional sequences of the polynucleotide inserts of a subset of said plurality of clones, and (iii) reagent specifications of said subset of clones; entering, in a graphical user interface, a query relating to one or more of said sequences or reagent specifications; determining matches between said query entry and said information; and displaying the results of said determination.
- 16. The method of claim 15, wherein the reagent specifications include physical data and ordering information for said subset of clones.
- 17. The method of claim 16, wherein said physical data and ordering information for a clone from said subset of clones includes the clone's processing history, availability, and location.
- 18. The method of claim 15, wherein said clones are CDNA clones.
- 19. A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database having records containing information identifying
(i) initial sequences of polynucleotide inserts of a plurality of clones, and (ii) reagent specifications of a subset of said plurality of clones.
- 20. The computer program product of claim 19, wherein the reagent specifications include physical data and ordering information for said subset of clones.
- 21. The computer program product of claim 20, wherein said physical data and ordering information for a clone from said subset of clones includes the clone's processing history, availability, and location.
- 22. The computer program product of claim 19, wherein said clones are cDNA clones.
- 23. A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database having records containing information identifying
(i) initial sequences of polynucleotide inserts of a plurality of clones, (ii) additional sequences of the polynucleotide inserts of a subset of said plurality of clones, and (iii) reagent specifications of said subset of clones.
- 24. The computer program product of claim 23, wherein the reagent specifications include physical data and ordering information for said subset of clones.
- 25. The computer program product of claim 24, wherein said physical data and ordering information for a clone from said subset of clones includes the clone's processing history, availability, and location.
- 26. The computer program product of claim 23, wherein said clones are cDNA clones.
- 27. A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database having records containing information identifying
(i) initial sequences of polynucleotide inserts of a plurality of clones, and (ii) reagent specifications of a subset of said plurality of clones;
the computer program product comprising computer-readable program code for effecting the following steps within a computing system: providing an interface for receiving a query relating to one or more reagent specifications; determining matches between said query entry and said information; and displaying the results of said determination.
- 28. The computer program product of claim 27, wherein the reagent specifications include physical data and ordering information for said subset of clones.
- 29. The computer program product of claim 28, wherein said physical data and ordering information for a clone from said subset of clones includes the clone's processing history, availability, and location.
- 30. The computer program product of claim 27, wherein said clones are cDNA clones.
- 31. A computer program product, comprising a computer-usable medium having computer-readable program code embodied thereon relating to a relational database having records containing information identifying
(i) initial sequences of polynucleotide inserts of a plurality of clones, (ii) additional sequences of the polynucleotide inserts of a subset of said plurality of clones, and (iii) reagent specifications of said subset of clones;
the computer program product comprising computer-readable program code for effecting the following steps within a computing system:
providing an interface for receiving a query relating to one or more reagent specifications; determining matches between said query entry and said information; and displaying the results of said determination.
- 32. The computer program product of claim 31, wherein the reagent specifications include physical data and ordering information for said subset of clones.
- 33. The computer program product of claim 32, wherein said physical data and ordering information for a clone from said subset of clones includes the clone's processing history, availability, and location.
- 34. The computer program product of claim 31, wherein said clones are cDNA clones.
- 35. A method, at least partially implemented on a computer system, for establishing a set of reagent clones, comprising:
grouping initial sequences of polynucleotide inserts in a plurality of clones into a master cluster; assembling the initial sequences of the master cluster into one or more contiguous sequences, such that relationships of sequences to each other in the master cluster are elucidated; and nominating at least one clone represented by a master cluster as a reagent clone, according to specified priority criteria.
- 36. The method of claim 35, wherein said initial sequences group into a plurality of master clusters.
- 37. The method of claim 36, wherein each master cluster represents a gene in a genome.
- 38. The method of claim 36, wherein said plurality of master clusters represent a fraction of the genes in a genome.
- 39. The method of claim 36, wherein said plurality of master clusters represent a fraction of the genes in the human genome.
- 40. The method of claim 36, wherein said plurality of master clusters represent a majority of the genes in the human genome.
- 41. The method of claim 36, wherein said plurality of master clusters represent substantially all of the genes in the human genome.
- 42. The method of claim 36, wherein said plurality of master clusters represent all of the genes in the human genome.
- 43. The method of claim 35, further comprising verifying the quality of a nominated clone by laboratory processes.
- 44. The method of claim 43, wherein said laboratory processes comprise verifying that the clone is viable and can grow to amounts suitable for isolating the clone's polynucleotide insert sequence.
- 45. The method of claim 44, further comprising resequencing said clone's polynucleotide insert sequence using 5′ and 3′ long read sequencing.
- 46. The method of claim 45, further comprising comparing the initial sequence of said nominated clone to the 5′ long read sequence to confirm the validity of said nominated clone.
- 47. The method of claim 43, wherein, if the quality of said nominated clone is not verified, another clone is nominated until a master cluster is represented by at least one clone whose quality is verified.
- 48. The method of claim 46, wherein, if the quality of said nominated clone is not verified, another clone is nominated until a master cluster is represented by at least one clone whose quality is verified.
- 49. The method of claim 35, wherein said priority criteria comprise:
(1) a clone associated with a 5′-most initial sequence in an assembly; (2) a clone having an insert in a pINCY vector, such that if the 5′-most clone in the assembly is not a pINCY clone, the 5′-most pINCY clone is nominated if it is no more than 150 bases shorter than the 5′-most clone; and (3) if the polynucleotide sequences of a cluster do not assemble, then the most recently sequenced clone insert in a pINCY vector is nominated.
- 50. A reagent clone identified by a process, at least partially implemented on a computer system, for establishing a set of reagent clones, comprising:
grouping initial sequences of polynucleotide inserts in a plurality of clones into a master cluster; assembling the initial sequences of the master cluster into one or more contiguous sequences, such that relationships of sequences to each other in the master cluster are elucidated; and nominating at least one clone represented by a master cluster as a reagent clone, according to specified priority criteria.
- 51. A reagent clone according to claim 50, wherein said priority criteria comprise:
(1) a clone associated with a 5′-most initial sequence in an assembly; (2) a clone having an insert in a pINCY vector, such that if the 5′-most clone in the assembly is not a pINCY clone, the 5′-most pINCY clone is nominated if it is no more than 150 bases shorter than the 5′-most clone; and (3) if the polynucleotide sequences of a cluster do not assemble, then the most recently sequenced clone insert in a pINCY vector is nominated.
- 52. A set of reagent clones identified by a process, at least partially implemented on a computer system, for establishing a set of reagent clones, comprising:
grouping initial sequences of polynucleotide inserts in a plurality of clones into a plurality of master clusters; assembling the initial sequences of the master clusters into one or more contiguous sequences per master cluster, such that relationships of sequences to each other in the master clusters are elucidated; and nominating at least one clone represented by each of a plurality of the master clusters as a set of reagent clones, according to specified priority criteria.
- 53. A set of reagent clones in accordance with claim 52, wherein said reagent set is used as hybridizable elements in a microarray.
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] The present application claims priority to U.S. Provisional Patent Application Serial No. 60/040,033 entitled RELATIONAL DATABASE FOR STORING BIOMOLECULAR SEQUENCE AND REAGENT INFORMATION, filed Mar. 5, 1997, and to U.S. Provisional Patent Application Serial No. 60/______ (Attorney Docket No. ICYTP007A+) entitled BIOMOLECULAR SEQUENCE AND REAGENT INFORMATION RELATIONAL DATABASES AND SYSTEMS, filed Mar. 3, 1998, both of which are herein incorporated by reference for all purposes.
[0002] The present application is also a continuation-in-part of U.S. patent application Ser. No. 08/947,845 entitled RELATIONAL DATABASE FOR STORING BIOMOLECULE INFORMATION, filed Oct. 9, 1997, the disclosure of which is herein incorporated by reference for all purposes.
Provisional Applications (2)
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Number |
Date |
Country |
|
60040033 |
Mar 1997 |
US |
|
60076682 |
Mar 1998 |
US |
Continuations (1)
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Number |
Date |
Country |
Parent |
09034807 |
Mar 1998 |
US |
Child |
10358905 |
Feb 2003 |
US |
Continuation in Parts (1)
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Number |
Date |
Country |
Parent |
08947845 |
Oct 1997 |
US |
Child |
10358905 |
Feb 2003 |
US |