Method and systems for processing polymeric sequence data and related information

• US 9,177,099 B2
• Filed: 08/31/2011
• Issued: 11/03/2015
• Est. Priority Date: 08/31/2010
• Status: Active Grant

• Current Assignee: Sala, Inc.
• Original Assignee: Annai Systems Inc
• Inventors: Ganeshalingam, Lawrence, Allen, Patrick Nikita
• Primary Examiner(s): Clow, Lori A
• Application Number:
  US13/223,071
• Publication Number:
  US 20120089652A1
• Time in Patent Office: 1,525 Days
• US Class Current: 1/1
• CPC Class Codes: G06F 16/22 Indexing; Data structures therefor; Storage structures
• 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 50/00 ICT programming tools or database systems specially adapted for bioinformatics
• CPC Class Codes: G16B 50/50 Compression of genetic data

Abstract

Methods and systems for organizing, representing and processing polymeric sequence information, including biopolymeric sequence information such as DNA sequence information and related information are disclosed herein. Polymeric sequence and associated information may be represented using a plurality of data units, each of which includes one or more headers and a payload containing a representation of a segment of the polymeric sequence. Each header may include or be linked to a portion of the associated information.

Claims

1. A biological sequence processing system, comprising:

a network interface configured to receive a query;

a data container having a data structure which facilitates processing of biological sequence data in the biological sequence processing system, the data container including a plurality of biological data units associated with the data container, each of the plurality of biological data units being packetized and used within the processing system and including;

a payload containing segmented biological sequence data,

a first BioIntelligent™

header associated with biological information relating to the segmented biological sequence data wherein the first BioIntelligent™

header identifies a first biological characteristic associated with a first subset of the segmented biological sequence data, and

a second BioIntelligent™

header identifying a second biological characteristic associated with a second subset of the segmented biological sequence data; and

a processor for executing codes of a computer program to;

process the query by querying at least one of the first BioIntelligent™

header and the second BioIntelligent™

header of at least one of the plurality of biological data units without examining the payload of the at least one of the plurality of biological data units, thereby improving computational efficiency; and

generate a response to the query using at least one of the first BioIntelligent™

header of the at least one of the plurality of biological data units and the second BioIntelligent™

header of the at least one of the plurality of biological data units;

wherein the network interface at least one of transmits and receives a signal containing a data packet including the response to the query.

2. The biological sequence processing system of claim 1 wherein the segmented biological sequence data comprises segmented genomic sequence data.

3. The biological sequence processing system of claim 1 wherein the at least one header is linked to the segmented biological sequence data.

4. The biological sequence processing system of claim 1 wherein the biological information identifies one or more portions of the segmented biological sequence data associated with a disease condition.

5. The biological sequence processing system of claim 1 wherein the biological information comprises one or more characteristics of the segmented biological sequence data.

6. The biological sequence processing system of claim 5 wherein the segmented biological sequence data comprises a segment of DNA sequence data.

7. The biological sequence processing system of claim 6 wherein the one or more characteristics relate to a property of the segment of DNA sequence data.

8. The biological sequence processing system of claim 7 wherein the property comprises a number of exons included within the segment of DNA sequence data.

9. The biological sequence processing system of claim 7 wherein the property comprises locations of exons included within the segment of DNA sequence data.

10. The biological sequence processing system of claim 7 wherein the property relates to an extent of methylation within the segment of DNA sequence data.

11. The biological sequence processing system of claim 7 wherein the property comprises one or more molecular pathways associated with the segment of DNA sequence data.

12. The biological sequence processing system of claim 7 wherein the property relates to one or more gene mutations within the segment of DNA sequence data.

13. The biological sequence processing system of claim 7 wherein the property relates to an association of a disease condition with the one or more gene mutations.

14. The biological sequence processing system of claim 13 wherein the first header includes first biological information relating to a property of the first segment of biological sequence data.

15. The biological sequence processing system of claim 14 wherein the first header includes second biological information relating to a property of the second segment of biological sequence data.

16. The biological sequence processing system of claim 1 wherein:

a first of the plurality of biological data units includes a first segment of biological sequence data and a first header;

a second of the plurality of biological data units includes a second segment of biological sequence data and a second header; and

wherein the first header includes first biological information relating to a property of the second segment of biological sequence data.

17. The biological sequence processing system of claim 16 wherein the first segment of biological sequence data comprises a first segment of DNA sequence data.

18. The biological sequence processing system of claim 17 wherein the property corresponds to a mutation of a gene included within the second segment of biological sequence data.

19. The biological sequence processing system of claim 18 wherein the mutation has an effect upon expression of a gene product associated with the first segment of DNA sequence data.

20. The biological sequence processing system of claim 19 wherein the second segment of biological sequence data comprises a segment of microRNA sequence data.

21. The biological sequence processing system of claim 16 wherein the second segment of biological sequence data comprises a second segment of DNA sequence data.

22. The biological sequence processing system of claim 21 wherein the second segment of biological sequence data comprises a first segment of RNA sequence data.

23. The biological sequence processing system of claim 16 wherein a third of the plurality of biological data units includes a third segment of biological sequence data and a third header wherein the first header points to the third header.

24. The biological sequence processing system of claim 1 wherein:

a first of the plurality of biological data units includes a first segment of biological sequence data and a first header;

a second of the plurality of biological data units includes a second segment of biological sequence data and a second header; and

a third of the plurality of biological data units includes a third segment of biological sequence data and a third header;

wherein the first header points to the second header and the second header points to the third header.

25. The biological sequence processing system of claim 24 wherein the first header also points to the third header.

26. The biological sequence processing system of claim 1 wherein the segmented biological sequence data within at least one of the plurality of biological data units comprises synthetic biological sequence data.

27. A polymeric sequence processing system, comprising:

a network interface configured to receive a query;

a data container having a data structure which facilitates processing of polymeric sequence data in the polymeric sequence processing system, the data container including a plurality of polymeric data units associated with the data container, each of the plurality of polymeric data units being packetized for and used within the processing system and including;

a payload containing segmented polymeric sequence data,

a first BioIntelligent™

header associated with information relating to the segmented polymeric sequence data wherein the first BioIntelligent™

header identifies a first biological characteristic associated with a first subset of the segmented polymeric sequence data, and

a second BioIntelligent™

header identifying a second biological characteristic associated with a second subset of the segmented polymeric sequence data;

a processor for executing codes of a computer program to;

process the query by querying at least one of the first BioIntelligent™

header and the second BioIntelligent™

header of at least one of the plurality of polymeric data units and without examining the payload of the at least one of the plurality of polymeric data units, thereby improving computational efficiency; and

generate a response to the query using at least one of the first BioIntelligent™

header of the at least one of the plurality of polymeric data units and the second BioIntelligent™

header of the at least one of the plurality of polymeric data units;

wherein the network interface at least one of transmits and receives a signal containing a data packet including the response to the query.

28. The polymeric sequence processing system of claim 27 wherein the segmented polymeric sequence data comprises segmented biopolymeric sequence data.

29. The polymeric sequence processing system of claim 27 wherein the at least one header is linked to the segmented polymeric sequence data.

30. A biological sequence processing system, comprising:

a network interface;

a data container having a data structure which facilitates processing of biological sequence data within the biological sequence processing system, the data container including;

a plurality of biological data units associated with the data container, each of the plurality of biological data units being packetized and used within the processing system and including;

a payload containing segmented biological sequence data, and

a set of BioIntelligent™

headers associated with information relating to the segmented biological sequence data wherein a first BioIntelligent™

header within the set of BioIntelligent™

headers identifies a first biological characteristic associated with a first subset of the segmented biological sequence data and a second BioIntelligent™

header within the set of BioIntelligent™

headers identifies a second biological characteristic associated with a second subset of the segmented biological sequence data; and

a processor for executing codes of a computer program to;

process the query by querying at least one of the first BioIntelligent™

header and the second BioIntelligent™

header of at least one of the plurality of biological data units without examining the payload of the at least one of the plurality of biological data units, thereby improving computational efficiency; and

generate a response to the query using at least one of the first BioIntelligent™

header of the at least one of the plurality of biological data units and the second BioIntelligent™

header of the at least one of the plurality of biological data units;

wherein the network interface at least one of transmits and receives a signal containing a data packet including the response to the query.

31. The biological sequence processing system of claim 30 wherein the segmented biological sequence data comprises segmented genomic sequence data.

32. The biological sequence processing system of claim 31 wherein at least a portion of the information comprises gene expression data.

33. The biological sequence processing system of claim 31 wherein at least a portion of the information comprises microarray data.

34. The biological sequence processing system of claim 30 wherein the set of headers for each one of the biological data units is linked to the segmented biological sequence data for each said one of the biological data units.

35. The biological sequence processing system of claim 30 wherein each header included within each set of headers is associated with one of a plurality of layers of a biological data model.

36. The biological sequence processing system of claim 35 wherein a first of the plurality of layers comprises a DNA layer.

37. The biological sequence processing system of claim 35 wherein a second of the plurality of layers comprises an RNA layer.

38. The biological sequence processing system of claim 37 wherein a third of the plurality of layers comprises a peptide layer.

39. The biological sequence processing system of claim 35 wherein one of the plurality of layers comprises a DNA layer.

40. The biological sequence processing system of claim 35 wherein one of the plurality of layers comprises an RNA layer.

41. The biological sequence processing system of claim 35 wherein one of the plurality of layers comprises a peptide layer.

42. The biological sequence processing system of claim 35 wherein one of the plurality of layers comprises a field-specific layer.

43. The biological sequence processing system of claim 35 wherein one of the plurality of layers comprises an application layer.

44. The biological sequence processing system of claim 35 wherein one of the plurality of layers comprises a user-specific layer.

45. The biological sequence processing system of claim 35 wherein a first of the plurality of layers comprises a DNA layer.

46. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer comprises methylation pattern information.

47. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer comprises chromosomal rearrangement information.

48. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer comprises at least one of an exon starting location and an exon ending location within the segmented biological sequence data.

49. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer comprises a number of exons included within the segmented biological sequence data.

50. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer represents at least one gene mutation in the segmented biological sequence data associated with a disease.

51. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer identifies at least one gene within the segmented biological sequence data.

52. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer identifies at least one of a tissue type and a cell type.

53. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer identifies one or more open reading frames within the segmented biological sequence data.

54. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer identifies at least one of a start position and an end position of the segmented biological sequence data.

55. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer identifies the segmented biological sequence data as being one of chromosomal and mitochondrial.

56. The biological sequence processing system of claim 45 wherein the information associated with one header of the set of headers relating to the DNA layer identifies at least one of a genus and a species of an organism from which the segmented biological sequence data originated.

57. The biological sequence processing system of claim 30 wherein a first of the plurality of biological data units includes a first set of headers wherein a first header of the first set of headers contains information relating to an alternative splicing event associated with one of a disease and a phenotype.

58. The biological sequence processing system of claim 30 wherein:

a first of the plurality of biological data units includes a first segment of biological sequence data and a first set of headers;

a second of the plurality of biological data units includes a second segment of biological sequence data and a second set of headers; and

wherein at least one of the first set of headers includes first biological information relating to at least one property of the second segment of biological sequence data.

59. The biological sequence processing system of claim 58 wherein a fourth of the plurality of layers comprises a field-specific layer.

60. The biological sequence processing system of claim 59 wherein a fifth of the plurality of layers comprises an application layer.

61. The biological sequence processing system of claim 30 wherein at least a portion of the information comprises medical records data.

62. The biological sequence processing system of claim 30 wherein at least a portion of the information comprises molecular pathways information.

63. The biological sequence processing system of claim 30 wherein the information is contained within each said set of headers.

64. The biological sequence processing system of claim 30 wherein a header included within at least one said set of headers includes a pointer to a location in a memory storing at least a part of the information.

65. The biological sequence processing system of claim 30 wherein the segmented biological sequence data for each of the biological data units is stored within a first memory element and the set of headers for each of the biological data units is stored within a second memory element.

66. The biological sequence processing system of claim 30 wherein the segmented biological sequence data comprises a sequence of nucleotide bases wherein each of the nucleotide bases is represented in a two-bit format.

67. The biological sequence processing system of claim 30 wherein the information comprises one or more of medical, clinical, pharmaceutical, environmental and experimental data.

68. The biological sequence processing system of claim 67 wherein the information further includes test results.

69. The biological sequence processing system of claim 30 wherein the segmented biological sequence data within at least one of the plurality of biological data units comprises synthetic biological sequence data.

70. A sequence processing system, comprising:

a network interface;

a data container having a data structure which facilitates processing of monomer sequence data within the sequence processing system, the data container including;

a plurality of polymeric data units associated with the data container, each of the plurality of polymeric data units being packetized and used within the processing system and including;

a payload containing a representation of at least a portion of a monomer sequence of a polymeric molecule, and

a set of BioIntelligent™

headers associated with information relating to the at least a portion of the monomer sequence wherein a first BioIntelligent™

header within the set of BioIntelligent™

headers identifies a first biological characteristic associated with a first subset of the monomer sequence and a second BioIntelligent™

header within the set of BioIntelligent™

headers identifies a second biological characteristic associated with a second subset of the monomer sequence; and

a processor for executing codes of a computer program to;

process the query by querying at least one of the first BioIntelligent™

header and the second BioIntelligent™

header of at least one of the plurality of polymeric data units without examining the payload of the at least one of the plurality of polymeric data units, thereby improving computational efficiency; and

generate a response to the query using at least one of the first BioIntelligent™

header of the at least one of the plurality of polymeric data units and the second BioIntelligent™

header of the at least one of the plurality of polymeric data units;

wherein the network interface at least one of transmits and receives a signal containing a data packet including the response to the query.

71. The sequence processing system of claim 70 wherein a header included within at least one said set of headers includes a pointer to a location in a memory storing at least a part of the information.

72. A biological sequence processing system, comprising:

a network interface;

a data container having a data structure which facilitates processing of biological sequence data within the biological sequence processing system, the data container including;

a first biological data unit associated with the data container wherein the first biological data unit includes first segmented biological sequence data and a first BioIntelligent™

header identifying a first biological characteristic associated with a first subset of the first segmented biological sequence data and a second BioIntelligent™

header identifying a second biological characteristic associated with a second subset of the first segmented biological sequence data, the first BioIntelligent™

header being different from the first segmented biological sequence data and identifying a first type of organism associated with the first biological sequence data; and

a second biological data unit associated with the data container wherein the second biological data unit includes second segmented biological sequence data and a third BioIntelligent™

header identifying a third biological characteristic associated with a first subset of the second segmented biological sequence data and a fourth BioIntelligent™

header identifying a fourth biological characteristic associated with a second subset of the second segmented biological sequence data, the third BioIntelligent™

header being different from the second segmented biological sequence data and identifying a second type of organism associated with the second biological sequence data wherein the first type of organism is different from the second type of organism; and

a processor for executing codes of a computer program to;

process the query by querying at least one of the first BioIntelligent™

header and the second BioIntelligent™

header without examining the first segmented biological sequence data, thereby improving computational efficiency; and

generate a response to the query using at least one of the first BioIntelligent™

header and the second BioIntelligent™

header;

wherein the network interface at least one of transmits and receives a signal containing a data packet including the response to the query.

73. The biological sequence processing system of claim 72 wherein the first type of organism comprises homo sapiens.

74. The biological sequence processing system of claim 73 wherein the second type of organism comprises bacteria.

75. The biological sequence processing system of claim 72 wherein the first biological data unit further includes a first plurality of headers, each of the first plurality of headers being associated with information relating to the first biological sequence data.

76. The biological sequence processing system of claim 75 wherein each header included within the first plurality of headers is associated with one of a plurality of layers of a biological data model.

77. The biological sequence processing system of claim 72 wherein the first biological sequence data comprises genomic sequence data.

78. A sequence data processing system including a data container having a data structure which accommodates polymeric sequence data, the sequence data processing system comprising:

a network interface;

a computer program product comprising a computer-readable medium including codes for causing the processor to;

receive, from a network-connected source of polymeric sequence data, segmented polymeric sequence data;

generate a plurality of polymeric data units, each of the plurality of polymeric data units including;

a payload containing segmented polymeric sequence data,

a first BioIntelligent™

header identifying a first biological characteristic associated with a first subset of the segmented polymeric sequence data and a second BioIntelligent™

header identifying a second biological characteristic associated with a second subset of the segmented polymeric sequence data;

store the plurality of polymeric data units within the data container; and

a processor for executing codes of a computer program to;

process the query by querying at least one of the first BioIntelligent™

header and the second BioIntelligent™

header of at least one of the plurality of polymeric data units without examining the payload of the at least one of the plurality of polymeric data units, thereby improving computational efficiency; and

generate a response to the query using at least one of the first BioIntelligent™

header of the at least one of the plurality of polymeric data units and the second BioIntelligent™

header of the at least one of the plurality of polymeric data units;

wherein the information is different from the segmented polymeric sequence and wherein the network interface at least one of transmits and receives a signal containing a data packet including the response to the query.