Database and system for storing, comparing and displaying genomic information

• US 5,966,712 A
• Filed: 05/15/1997
• Issued: 10/12/1999
• Est. Priority Date: 12/12/1996
• Status: Expired due to Fees

• Current Assignee: Incyte Genomics, Inc. (Incyte Corporation)
• Original Assignee: Incyte Pharmaceuticals, Inc. (Incyte Corporation)
• Inventors: Klingler, Tod M., Heath, Joe Don, Russo, Frank D., Sabatini, Cathryn E., Berry, Stephanie F., Covitz, Peter A.
• Primary Examiner(s): Choules, Jack M.
• Application Number:
  US08/857,382
• Time in Patent Office: 880 Days
• Field of Search: 707/104, 707/10, 707/6, 435/6
• US Class Current: N/A
• 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 30/20 Sequence assembly
• 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 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• CPC Class Codes: G16B 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: Y10S 707/99945 Object-oriented database structure processing
• CPC Class Codes: Y10S 707/99948 Application of database or data structure, e.g. distributed, multimedia, or image

Abstract

Disclosed is a relational database system for storing and manipulating biomolecular sequence information, the database including genomic libraries for a plurality of types of organisms, the libraries having multiple genomic sequences, at least some of which represent open reading frames located along a contiguous sequence on each the plurality of organisms'"'"' genomes, and a user interface capable of receiving a selection of two or more of the genomic libraries for comparison and displaying the results of the comparison. The system also provides a user interface capable of receiving a selection of one or more probe open reading frames for use in determining homologous matches between such probe open reading frame(s) and the open reading frames in the genomic libraries, and displaying the results of the determination.

Claims

1. A method of comparing genetic complements of different types of organisms, the method comprising:

providing a database including sequence libraries for a plurality of types of organisms, said libraries having multiple biomolecular sequences, at least some of which represent open reading frames located along one or more contiguous sequences on each of the plurality of organisms'"'"' genomes;

receiving a selection of two or more of said sequence libraries for comparison;

determining open reading frames common or unique to the selected sequence libraries; and

displaying the results of said determination.

2. The method of claim 1, wherein the database includes biomolecular sequences from a microbial organism.

3. The method of claim 1 wherein the biomolecular sequences include nucleic acid sequences.

4. The method of claim 3, wherein the nucleic acid sequences include genomic sequences.

5. The method of claim 4, wherein the genomic sequences are microbial genomic sequences.

6. The method of claim 1, wherein the biomolecular sequences include peptide sequences.

7. The method of claim 1, wherein the step of receiving a selection of two or more of said sequence libraries for comparison includes receiving a user selection from two or more pull-down menus in a graphical user interface.

8. The method of claim 1, wherein the displaying step displays a unique identifier for a group of related opening reading frames.

9. The method of claim 8, wherein the display further comprises annotated information relating to the group of related open reading frames obtained from a public database.

10. The method of claim 1, wherein the open reading frames common to the selected libraries are determined and displayed.

11. The method of claim 1, wherein the open reading frames unique to a particular selected library are determined and displayed.

12. A method of comparing genomic complements of different types of organisms, the method comprising:

providing a database including genomic libraries for a plurality of types of organisms, said libraries having multiple genomic sequences, at least some of which represent at least portions of open reading frames located along one or more contiguous sequences on each of the plurality of organisms'"'"' genomes;

receiving a selection of two or more of said genomic libraries for comparison;

determining sequences common or unique to the selected genomic libraries; and

displaying the results of said determination.

13. The method of claim 12, wherein the genomic sequences are microbial genomic sequences.

14. The method of claim 12, wherein the step of receiving a selection of two or more of said sequence libraries for comparison includes receiving a user selection from two or more pull-down menus in a graphical user interface.

15. The method of claim 12, wherein the displaying step displays a unique identifier for a group of related opening reading frames.

16. The method of claim 15, wherein the display further comprises annotated information relating to the group of related opening reading frames obtained from a public database.

17. The method of claim 12, wherein said results are displayed as groupings of related open reading frames.

18. The method of claim 12, wherein the open reading frames common to the selected genomic libraries are determined and displayed.

19. The method of claim 12, wherein the open reading frames unique to a particular selected genomic library are determined and displayed.

20. A method of identifying genes common to a set of organisms, the method comprising:

providing a database including genomic libraries for a plurality of types of organisms, said libraries having multiple genomic sequences, at least some of which represent open reading frames located along one or more contiguous sequences on each the plurality of organisms'"'"' genomes;

displaying at least one list of said genomic libraries;

receiving a user'"'"'s selection of one or more genomic libraries from said at least one list;

determining sequences common to the selected genomic libraries; and

displaying the results of said determination.

21. The method of claim 20, wherein the displaying step displays a unique identifier for a group of related opening reading frames.

22. The method of claim 20, wherein the genomic sequences are microbial genomic sequences.

23. A method of identifying genes common to one or more in a set of organisms, the method comprising:

providing a database including genomic libraries for a plurality of types of organisms, said libraries having multiple genomic sequences, at least some of which represent open reading frames located along one or more contiguous sequences on each the plurality of organisms'"'"' genomes;

displaying one or more lists of said genomic libraries;

receiving a user'"'"'s selection of from none to all the genomic libraries from each of said lists;

determining sequences common to the selected genomic libraries from a first list or group of lists and absent in the genomic libraries of one or more other lists; and

displaying the results of said determination.

24. The method of claim 23, wherein there are two lists of genomic libraries displayed.

25. The method of claim 23, wherein the second displaying step displays a unique identifier for a group of related opening reading frames.

26. The method of claim 23, wherein one library is selected from said first list or group of lists, and the remaining libraries are selected from said one or more other lists.

27. The method of claim 23, wherein the genomic sequences are microbial genomic sequences.

28. A computer system comprising:

a database including genomic libraries for a plurality of types of organisms, said libraries having multiple genomic sequences, at least some of which represent open reading frames located along one or more contiguous sequences on each the plurality of organisms'"'"' genomes; and

a user interface capable of receiving a selection of two or more of said genomic libraries for comparison and displaying the results of said comparison.

29. The computer system of claim 28, wherein the genomic sequences are microbial genomic sequences.

30. A method of identifying libraries in which a given gene exists, the method comprising:

providing a database including genomic libraries for one or more types of organisms, said libraries having multiple genomic sequences, at least some of which represent open reading frames located along one or more contiguous sequences on each the one or more organisms'"'"' genomes;

receiving a selection of one or more probe sequences;

determining homologous matches between said probe sequences and the sequences in said genomic libraries; and

displaying the results of said determination.

31. The method of claim 30, wherein said probe sequences and said library sequences are open reading frames.

32. The method of claim 30, wherein said results are displayed as groupings of related open reading frames.

33. The method of claim 30, wherein the genomic sequences are microbial genomic sequences.

34. A computer system, comprising:

a database including genomic libraries for one or more types of organisms, said libraries having multiple genomic sequences, at least some of which represent open reading frames located along one or more contiguous sequences on each the plurality of organisms'"'"' genomes;

a user interface capable of receiving a selection of one or more probe sequences for use in determining homologous matches between said one or more probe sequences and the sequences in said genomic libraries, and displaying the results of said determination.

35. The computer system of claim 34, wherein the genomic sequences are microbial genomic sequences.

36. A computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to a database including genomic libraries for one or more types of organisms, said libraries having multiple genomic sequences, at least some of which represent open reading frames located along one or more contiguous sequences on each the one or more organisms'"'"' genomes, the computer program product comprising computer-readable program code for effecting the following steps within a computing system:

providing an interface for receiving a selection of two or more of said genomic libraries for comparison;

determining sequences common or unique to the selected genomic libraries; and

displaying the results of said determination.

37. The computer program product of claim 36, wherein the sequences in said determining step are open reading frames.

38. The computer program product of claim 36, wherein the genomic sequences are microbial genomic sequences.

39. A computer program product comprising a computer-usable medium having computer-readable program code embodied thereon relating to a database including genomic libraries for one or more types of organisms, said libraries having multiple genomic sequences, at least some of which represent open reading frames located along one or more contiguous sequences on each the one or more organisms'"'"' genomes, the computer program product comprising computer-readable program code for effecting the following steps within a computing system:

providing an interface for receiving a selection of one or more probe open reading frames;

determining homologous matches between said probe sequences and the sequences in said genomic libraries; and

displaying the results of said determination.

40. The computer program product of claim 39, wherein said probe and said library sequences in said determining step are open reading frames.

41. The computer program product of claim 39, wherein the genomic sequences are microbial genomic sequences.

42. A method of presenting the genetic complement of an organism, the method comprising:

providing a database including sequence libraries for a plurality of types of organisms, said libraries having multiple biomolecular sequences, at least some of which represent open reading frames located along one or more contiguous sequences on each of the plurality of organisms'"'"' genomes;

receiving a selection of one of said sequence libraries;

determining open reading frames within the selected sequence library; and

displaying the results of said determination as one or more unique identifiers for groups of related opening reading frames.

43. The method of claim 42, wherein the display further comprises annotated information relating to the group of related opening reading frames obtained from a public database.

44. The method of claim 42, wherein the genomic sequences are microbial genomic sequences.