Method and systems for processing polymeric sequence data and related information

• US 9,177,100 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:
  US13/223,084
• Publication Number:
  US 20120095693A1
• 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 for processing polymeric sequence information, the apparatus comprising:

a data container structured to contain a plurality of packetized biological data units;

a network connection for receiving a plurality of polymeric sequence segments representative of polymeric sequence data, receiving a query relating to the polymeric sequence data, and sending a response to the query; and

a processor for executing codes of a computer program to;

create the plurality of packetized biological data units based upon the plurality of polymeric sequence segments, each of the packetized biological data units including one polymeric sequence segment of the plurality of polymeric sequence segments and a set of BioIntelligent™

biologically-relevant headers associated with information relating to the one polymeric sequence segment wherein the BioIntelligent™

biologically-relevant headers include first header information identifying a first biological characteristic associated with a first subset of the one polymeric sequence segment and second header information identifying a second biological characteristic associated with a second subset of the one polymeric sequence segment;

store the plurality of packetized biological data units within the data container;

process the query by querying the first header information and the second header information and without examining the plurality of polymeric sequence segments, thereby improving computational efficiency; and

generate the response to the query using at least a portion of the first header information and the second header information.

2. The apparatus of claim 1 wherein the codes of the computer program further cause the processor to sort ones of the plurality of packetized biological data units within the data container.

3. The apparatus of claim 1 wherein the codes of the computer program further cause the processor to classify ones of the plurality of packetized biological data units.

4. The apparatus of claim 1 wherein each said set of BioIntelligent™

biologically-relevant headers contains the information associated with the corresponding one polymeric sequence segment.

5. The apparatus of claim 1 wherein each said set of BioIntelligent™

biologically-relevant headers contains a pointer to a location in a memory storing at least a portion of the information associated with the corresponding one polymeric sequence segment.

6. The apparatus of claim 1 wherein each BioIntelligent™

biologically-relevant header included within each said set of BioIntelligent™

biologically-relevant headers is associated with one of a plurality of layers of a data model representative of the polymeric sequence data.

7. The apparatus of claim 6 wherein the one of the plurality of layers comprises a DNA layer.

8. The apparatus of claim 6 wherein the one of the plurality of layers comprises an RNA layer.

9. The apparatus of claim 6 wherein the one of the plurality of layers comprises a peptide layer.

10. The apparatus of claim 6 wherein the one of the plurality of layers comprises a field-specific layer.

11. The apparatus of claim 6 wherein the one of the plurality of layers comprises an application layer.

12. The apparatus of claim 6 wherein the one of the plurality of layers comprises a user-specific layer.

13. The apparatus of claim 1 wherein at least a portion of the information comprises medical records data.

14. The apparatus of claim 1 wherein at least a portion of the information comprises gene expression data.

15. The apparatus of claim 1 wherein at least a portion of the information comprises molecular pathways information.

16. A computer program product comprising a non-transitory computer readable medium including codes for causing a computer to:

receive a plurality of polymeric sequence segments representative of polymeric sequence data;

create a plurality of packetized biological data units based upon the plurality of polymeric sequence segments, each of the packetized biological data units including one polymeric sequence segment of the plurality of polymeric sequence segments and a set of BioIntelligent™

biologically-relevant headers associated with information relating to the one polymeric sequence segment wherein the BioIntelligent™

biologically-relevant headers include first header information identifying a first biological characteristic associated with a first subset of the one polymeric sequence segment and second header information identifying a second biological characteristic associated with a second subset of the one polymeric sequence segment; and

store the plurality of packetized biological data units within a data container;

process the query by querying the first header information and the second header information and without examining the plurality of polymeric sequence segments, thereby improving computational efficiency; and

generate the response to the query using at least a portion of the first header information and the second header information.

17. The non-transitory computer readable medium of claim 16 wherein the codes further include codes for causing the computer to sort ones of the plurality of packetized biological data units within the data container.

18. The non-transitory computer readable medium of claim 16 wherein the codes further include codes for causing the computer to classify ones of the plurality of packetized biological data units within the data container.