Method and systems for processing polymeric sequence data and related information

• US 9,189,594 B2
• Filed: 08/31/2011
• Issued: 11/17/2015
• Est. Priority Date: 08/31/2010
• Status: Active Grant

• Current Assignee: Sala, Inc.
• Original Assignee: Annai Systems Inc
• Inventors: Allen, Patrick Nikita, Ganeshalingam, Lawrence
• Primary Examiner(s): Clow, Lori A
• Application Number:
  US13/223,092
• Publication Number:
  US 20120089608A1
• Time in Patent Office: 1,539 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. A computer program product for use in a data processing system including a data container, the computer program product comprising a non-transitory computer readable medium including codes for causing a computer to:

segment polymeric sequence data into a plurality of polymeric sequence segments;

storing, within the data container, a plurality of packetized biological data units representative of the plurality of polymeric sequence segments wherein each of the plurality of packetized biological data units includes a set of BioIntelligent™

biologically-relevant headers identifying biological characteristics associated with portions of a corresponding one of the plurality of polymeric sequence segments;

use a set of classification rules to group the BioIntelligent™

biologically-relevant headers of a first set of packetized biological data units of the plurality of packetized biological data units into a first classification associated with a disease;

use the set of classification rules to group the BioIntelligent™

biologically-relevant headers of a second set of packetized biological data units of the plurality of packetized biological data units into a second classification;

perform a processing operation involving ones of the first set of packetized biological data units and the second set of packetized biological data units wherein the processing operation includes accessing ones of the BioIntelligent™

biologically-relevant headers of the first set of packetized biological data units and the BioIntelligent™

biologically-relevant headers of the second set of packetized biological data units without examining the plurality of polymeric sequence segments, thereby improving computational efficiency; and

transmit a result of the processing operation over a network.

2. The computer program product of claim 1 wherein the processing operation includes storing certain of the ones of the first set of packetized biological data units and the second set of polymeric data units in a first processing queue.

3. The computer program product of claim 2 further including:

storing other of the ones of the first set of packetized biological data units and the second set of packetized biological data units in a second processing queue; and

performing an additional processing operation involving the other of the ones of the first set of packetized biological data units and the second set of packetized biological data units.

4. The computer program product of claim 1 further including outputting, from the data container, certain of the ones of the first set of packetized biological data units and the second set of packetized biological data units in response to an instruction generated by an application program.

5. A computer-implemented method for use in a data processing system including a data container for storing a plurality of packetized biological data units, each of the plurality of packetized biological data units including segmented polymeric sequence data and at least one BioIntelligent™

biologically-relevant header identifying a biological characteristic associated with a portion of the segmented polymeric sequence data, the method comprising;

accessing, using a processor, first BioIntelligent™

biologically-relevant header information relating to at least one of a location or a subset of first segmented polymeric sequence data of a first packetized biological data unit included within the plurality of packetized biological data units wherein the first packetized biological data unit includes a first sequence identifier wherein the accessing the first BioIntelligent™

biologically-relevant header information is performed without examining the first segmented polymeric sequence data, thereby improving computational efficiency;

accessing, using the processor, second BioIntelligent™

biologically-relevant header information relating to at least one of a location or a subset of second segmented polymeric sequence data of a second packetized biological data unit included within the plurality of packetized biological data units wherein the second packetized biological data unit includes a second sequence identifier;

performing, using the processor, a classifying-operation involving the first BioIntelligent™

biologically-relevant header information and the second BioIntelligent™

header information wherein the classifying operation includes grouping the first BioIntelligent™

biologically-relevant header information and the second BioIntelligent™

biologically-relevant header information into a classification associated with a disease wherein at least a portion of the first segmented polymeric sequence data and at least a portion of the second segmented polymeric sequence segments is associated with the disease;

storing results of the classifying operation on a machine readable memory, wherein the results are used for biological or genetic research or for medical purposes;

transmitting the results of the classifying operation over a network.

6. The computer-implemented method of claim 5 further including storing the first BioIntelligent™

biologically-relevant header information and the second BioIntelligent™

biologically-relevant header information in a first processing queue.

7. The computer-implemented method of claim 6 further including storing, within a second processing queue, third BioIntelligent™

biologically-relevant header information associated with third segmented polymeric sequence data of a third packetized biological data unit included within the plurality of packetized biological data units and fourth BioIntelligent™

biologically-relevant header information associated with fourth segmented polymeric sequence data of a fourth packetized biological data unit included within the plurality of packetized biological data units.

8. The computer-implemented method of claim 7 further including performing an additional classifying operation involving the third BioIntelligent™

biologically-relevant header information and the fourth BioIntelligent™

biologically-relevant header information.

9. A computer program product for use in a data processing system including a data container for storing a plurality of packetized biological data units, each of the plurality of packetized biological data units including segmented polymeric sequence data and at least one BioIntelligent™

biologically-relevant header associated with information relating to the segmented polymeric sequence data, the computer program product comprising a non-transitory computer readable medium including codes for causing a computer to;

access first BioIntelligent™

biologically-relevant header information relating to at least one of a location or a subset of first segmented polymeric sequence data of a first packetized biological data unit included within the plurality of packetized biological data units without examining the first segmented polymeric sequence data, thereby improving computational efficiency;

access second BioIntelligent™

biologically-relevant header information relating to at least one of a location or a subset of second segmented polymeric sequence data of a second packetized biological data unit included within the plurality of packetized biological data units;

perform a classifying operation involving the first BioIntelligent™

header information and the second BioIntelligent™

header information wherein the classifying operation includes grouping the first BioIntelligent™

biologically-relevant header information and the second BioIntelligent™

biologically-relevant header information into a classification associated with a disease;

transmit a result of the classifying operation over a network.

10. The computer program product of claim 9 wherein the codes further include codes for causing the computer to store the first BioIntelligent™

header information and the second BioIntelligent™

biologically-relevant header information in a first processing queue.

11. The computer program product of claim 10 wherein the codes further include codes for causing the computer to store, within a second processing queue, third BioIntelligent™

biologically-relevant header information associated with third segmented polymeric sequence data of a third packetized biological data unit included within the plurality of packetized biological data units and to store fourth BioIntelligent™

biologically-relevant header information associated with fourth segmented polymeric sequence data of a fourth packetized biological data unit included within the plurality of packetized biological data units.

12. The computer program product of claim 11 wherein the codes further include codes for causing the computer to perform an additional processing operation involving the third BioIntelligent™

biologically-relevant header information and the fourth BioIntelligent™

biologically-relevant header information.

13. An apparatus, comprising:

a data container for storing a plurality of packetized biological data units, each of the plurality of packetized biological data units including segmented polymeric sequence data and at least one BioIntelligent™

biologically-relevant header associated with information relating to the segmented polymeric sequence data; and

a processor in communication with the data container, the processor being configured to;

access first BioIntelligent™

biologically-relevant header information relating to at least one of a location or a subset of first segmented polymeric sequence data of a first packetized biological data unit included within the plurality of packetized biological data units without examining the first segmented polymeric sequence data, thereby improving computational efficiency;

access second BioIntelligent™

biologically-relevant header information relating to at least one of a location or a subset of second segmented polymeric sequence data of a second packetized biological data unit included within the plurality of packetized biological data units without examining the second segmented polymeric sequence data, thereby improving computational efficiency;

perform a classifying operation involving the first BioIntelligent™

biologically-relevant header information and the second BioIntelligent™

biologically-relevant header information wherein the classifying operation includes grouping the first BioIntelligent™

biologically-relevant header information and the second BioIntelligent™

biologically-relevant header information into a classification associated with a disease wherein at least a portion of the first segmented polymeric sequence data and at least a portion of the second segmented polymeric sequence segment data is associated with the disease; and

a transmitter configured to transmit a result of the classifying operation over a network.

14. The apparatus of claim 13 wherein the processor is further configured to:

receive polymeric sequence data; and

generate the segmented polymeric sequence data by segmenting the polymeric sequence data in accordance with requirements of an application program executed by the processor.

15. The apparatus of claim 14 further including a processing queue wherein the processor is further configured to store the first BioIntelligent™

biologically-relevant header information and the second BioIntelligent™

biologically-relevant header information in a first processing queue.

16. The apparatus of claim 15 further including a second processing queue wherein the processor is further configured to store, within the second processing queue, third BioIntelligent™

biologically-relevant header information associated with third segmented polymeric sequence data of a third packetized biological data unit included within the plurality of packetized biological data units and fourth BioIntelligent™

biologically-relevant header information associated with fourth segmented polymeric sequence data of a fourth packetized biological data unit included within the plurality of packetized biological data units.