Method and systems for processing polymeric sequence data and related information

• US 9,177,101 B2
• Filed: 08/31/2011
• Issued: 11/03/2015
• Est. Priority Date: 08/31/2010
• Status: Active Grant

• Current Assignee: Annai Systems Inc
• Original Assignee: Annai Systems Inc
• Inventors: Ganeshalingam, Lawrence, Allen, Patrick Nikita
• Primary Examiner(s): Clow, Lori A
• Application Number:
  US13/223,097
• Publication Number:
  US 20120089603A1
• Time in Patent Office: 1,525 Days
• Field of Search: None
• 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. An apparatus, comprising:

a network interface;

a data container having a data structure accommodating a packetized biological data unit, the packetized biological data unit including;

first layer biological sequence data and a first BioIntelligent header comprising first information relating to a first biological characteristic of the first layer biological sequence data wherein the first biological characteristic is linked to at least one sequence location or segment of the first layer biological sequence data;

second layer biological sequence data and a second BioIntelligent header comprising second information relating to a second biological characteristic of the second layer biological sequence data wherein the second biological characteristic is linked to at least one sequence location or segment of the second layer biological sequence data and wherein the first layer biological sequence data and the second layer biological sequence data are respectively associated with a first layer and a second layer of a biological data model; and

a processor in communication with the data container, the processor being configured to execute computer code which, when executed by the processor, causes the processor to;

receive, via the network interface, a request sent by a requesting device;

process the request by accessing the first BioIntelligent header and the second BioIntelligent header in order to obtain the first information and the second information wherein the processing is performed without examining the first layer biological sequence data or the second layer biological sequence data, thereby improving computational efficiency,

generate a data packet including at least one of the first information and the second information,

transmit, via the network interface, the data packet to the requesting device.

2. The apparatus of claim 1 wherein the first layer biological sequence data comprises DNA sequence data and the second layer biological sequence data comprises RNA sequence data.

3. The apparatus of claim 1 wherein the first BioIntelligent header is linked to the first layer biological sequence data.

4. The apparatus of claim 1 wherein the first layer comprises a DNA layer.

5. The apparatus of claim 4 wherein the second layer comprises an RNA layer.

6. The apparatus of claim 1 wherein the first BioIntelligent header includes first header information pointing to second header information included within the second BioIntelligent header.

7. The apparatus of claim 1 wherein the first information identifies one or more portions of the first layer biological sequence data pertinent to the second layer biological sequence data.

8. The apparatus of claim 1 wherein the first layer biological sequence data comprises segmented biopolymeric sequence data.

9. The apparatus of claim 1 wherein the first information identifies one or more portions of the first layer biological sequence data associated with a disease condition.

10. An apparatus, comprising:

a network interface;

a data container having a data structure accommodating packetized biological data units, the data container storing;

a first packetized biological data unit including a first payload defining a first representation of first biological sequence data and at least a first BioIntelligent header comprising first biological information relating to a first biological characteristic of the first biological sequence data wherein the first biological characteristic is linked to at least one sequence location or segment of the first biological sequence data;

a second packetized biological data unit including a second payload defining a second representation of second biological sequence data and at least a second BioIntelligent header comprising second biological information relating to a second biological characteristic of the second biological sequence data wherein the first biological characteristic is linked to at least one sequence location or segment of the first biological sequence data and wherein the first biological sequence data is associated with a first layer of a biological data model and the second biological sequence data is associated with a second layer of the biological data model; and

a processor in communication with the data container, the processor being configured to execute computer code which, when executed by the processor, causes the processor to;

receive, via the network interface, a request sent by a requesting device;

process the request by accessing the first BioIntelligent header and the second BioIntelligent header in order to obtain the first biological information and the second biological information, wherein the processing is performed without examining the first biological sequence data or the second biological sequence data, thereby improving computational efficiency,

generate a data packet including at least one of the first biological information and the second biological information,

transmit, via the network interface, the data packet to the requesting device.

11. The apparatus of claim 10 wherein the first representation comprises a first instruction-based representation of the first biological sequence data contained within the first payload.

12. The apparatus of claim 11 wherein the second representation comprises a second instruction-based representation of the second biological sequence data contained within the second payload.

13. An apparatus, comprising:

a network interface;

a data container having a data structure accommodating packetized biological data units, the data container storing;

a first packetized biological data unit including a first representation of first biological sequence data and at least a first BioIntelligent header comprising first biological information relating to a first biological characteristic of the first biological sequence data wherein the first biological characteristic is linked to at least one sequence location or segment of the first biological sequence data;

a second packetized biological data unit including a second representation of second biological sequence data and at least a second BioIntelligent header comprising second biological information relating to a second biological characteristic of the second biological sequence data wherein the second biological characteristic is linked to at least one sequence location or segment of the second biological sequence data and wherein the first biological sequence data is associated with a first layer of a biological data model and the second biological sequence data is associated with a second layer of the biological data model; and

a processor in communication with the data container, the processor being configured to execute computer code which, when executed by the processor, causes the processor to;

receive, via the network interface, a request sent by a requesting device,

process the request by accessing, in response to the request, the first BioIntelligent header and the second BioIntelligent header in order to at least one of classify and group the first packetized biological data unit and the second packetized biological data unit wherein the processing is performed without examining the first biological sequence data or the second biological sequence data, thereby improving computational efficiency,

transmit, via the network interface, a data packet to the requesting device wherein the data packet includes at least one of the first BioIntelligent header and the second BioIntelligent header.

14. An apparatus, comprising:

a network interface

a data container having a data structure accommodating a packetized biological data unit, the packetized biological data unit including;

first biological sequence data and a first BioIntelligent header comprising first information relating to a first biological characteristic of the first layer biological sequence data wherein the first biological characteristic is linked to at least one sequence location or segment of the first biological sequence data;

second biological sequence data and a second BioIntelligent header comprising second information relating to a second biological characteristic of the second biological sequence data wherein the second biological characteristic is linked to at least one sequence location or segment of the second biological sequence data; and

a processor in communication with the data container, the processor being configured to execute computer code which, when executed by the processor, causes the processor to;

receive, via the network interface, the first information and the second information;

generate, using the first information and the second information, the packetized biological data unit;

store the packetized biological data unit within the data container;

process a request by accessing the first BioIntelligent header and the second BioIntelligent header wherein the processing is performed without examining the first biological sequence data or the second biological sequence data, thereby improving computational efficiency.

15. The apparatus of claim 14 wherein the computer code, when executed by the processor, further cause the processor to transmit, via the network interface, a data packet wherein the data packet includes at least one of the first BioIntelligent header and the second BioIntelligent header.