Method and systems for processing polymeric sequence data and related information

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.

We claim: 
     
         1 . A computer-readable medium for storing a data container having a data structure which facilitates processing of biological sequence data in a data processing system, the medium comprising:
 a plurality of biological data units associated with the data container, each of the plurality of biological data units including:   a payload containing segmented biological sequence data, and   at least one header associated with biological information relating to the segmented biological sequence data;   wherein the segmented biological sequence data of ones of the plurality of biological data units may be packetized with the biological information of ones of the plurality of biological data units for use within the data processing system.   
     
     
         2 . The computer-readable medium of  claim 1  wherein the segmented biological sequence data comprises segmented genomic sequence data. 
     
     
         3 . The computer-readable medium of  claim 1  wherein the at least one header is linked to the segmented biological sequence data. 
     
     
         4 . The computer-readable medium 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 computer-readable medium of  claim 1  wherein the biological information comprises one or more characteristics of the segmented biological sequence data. 
     
     
         6 . The computer-readable medium of  claim 5  wherein the segmented biological sequence data comprises a segment of DNA sequence data. 
     
     
         7 . The computer-readable medium of  claim 6  wherein the one or more characteristics relate to a property of the segment of DNA sequence data. 
     
     
         8 . The computer-readable medium of  claim 7  wherein the property comprises a number of exons included within the segment of DNA sequence data. 
     
     
         9 . The computer-readable medium of  claim 7  wherein the property comprises locations of exons included within the segment of DNA sequence data. 
     
     
         10 . The computer-readable medium of  claim 7  wherein the property relates to an extent of methylation within the segment of DNA sequence data. 
     
     
         11 . The computer-readable medium of  claim 7  wherein the property comprises one or more molecular pathways associated with the segment of DNA sequence data. 
     
     
         12 . The computer-readable medium of  claim 7  wherein the property relates to one or more gene mutations within the segment of DNA sequence data. 
     
     
         13 . The computer-readable medium 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. 
 
     
     
         14 . The computer-readable medium of  claim 13  wherein the first segment of biological sequence data comprises a first segment of DNA sequence data. 
     
     
         15 . The computer-readable medium of  claim 13  wherein the second segment of biological sequence data comprises a second segment of DNA sequence data. 
     
     
         16 . The computer-readable medium of  claim 15  wherein the second segment of biological sequence data comprises a first segment of RNA sequence data. 
     
     
         17 . The computer-readable medium of  claim 14  wherein the property corresponds to a mutation of a gene included within the second segment of biological sequence data. 
     
     
         18 . The computer-readable medium of  claim 17  wherein the mutation has an effect upon expression of a gene product associated with the first segment of DNA sequence data. 
     
     
         19 . The computer-readable medium of  claim 18  wherein the second segment of biological sequence data comprises a segment of microRNA sequence data. 
     
     
         20 . The computer-readable medium of  claim 13  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. 
     
     
         21 . The computer-readable medium of  claim 7  wherein the property relates to an association of a disease condition with the one or more gene mutations. 
     
     
         22 . The computer-readable medium 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. 
 
     
     
         23 . The computer-readable medium of  claim 22  wherein the first header also points to the third header. 
     
     
         24 . The computer-readable medium of  claim 21  wherein the first header includes first biological information relating to a property of the first segment of biological sequence data. 
     
     
         25 . The computer-readable medium of  claim 24  wherein the first header includes second biological information relating to a property of the second segment of biological sequence data. 
     
     
         26 . A computer-readable medium for storing a data container having a data structure which facilitates processing of polymeric sequence data in a data processing system, the medium comprising:
 a plurality of polymeric data units associated with the data container, each of the plurality of polymeric data units including:
 a payload containing segmented polymeric sequence data, and 
 at least one header associated with information relating to the segmented polymeric sequence data; 
   wherein the segmented polymeric sequence data of ones of the plurality of polymeric data units may be packetized with the information of ones of the plurality of polymeric data units for use within the data processing system.   
     
     
         27 . The computer-readable medium of  claim 26  wherein the segmented polymeric sequence data comprises segmented biopolymeric sequence data. 
     
     
         28 . The computer-readable medium of  claim 26  wherein the at least one header is linked to the segmented polymeric sequence data. 
     
     
         29 . The computer-readable medium 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. 
     
     
         30 . A computer-readable medium for storing a data container having a data structure which facilitates processing of biological sequence data within a data processing system, the medium comprising:
 a plurality of biological data units associated with the data container, each of the plurality of biological data units including:
 a payload containing segmented biological sequence data, and 
 a set of headers associated with information relating to the segmented biological sequence data; 
   wherein the segmented biological sequence data of ones of the plurality of biological data units may be packetized with the biological information of ones of the plurality of biological data units for use within the data processing system.   
     
     
         31 . The computer-readable medium of  claim 30  wherein the segmented biological sequence data comprises segmented genomic sequence data. 
     
     
         32 . The computer-readable medium 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. 
     
     
         33 . The computer-readable medium 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. 
     
     
         34 . The computer-readable medium of  claim 33  wherein a first of the plurality of layers comprises a DNA layer. 
     
     
         35 . The computer-readable medium of  claim 4  wherein a second of the plurality of layers comprises an RNA layer. 
     
     
         36 . The computer-readable medium of  claim 35  wherein a third of the plurality of layers comprises a peptide layer. 
     
     
         37 . The computer-readable medium 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. 
     
     
         38 . The computer-readable medium 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. 
 
     
     
         39 . The computer-readable medium of  claim 38  wherein a fourth of the plurality of layers comprises a field-specific layer. 
     
     
         40 . The computer-readable medium of  claim 39  wherein a fifth of the plurality of layers comprises an application layer. 
     
     
         41 . The computer-readable medium of  claim 33  wherein one of the plurality of layers comprises a DNA layer. 
     
     
         42 . The computer-readable medium of  claim 33  wherein one of the plurality of layers comprises an RNA layer. 
     
     
         43 . The computer-readable medium of  claim 33  wherein one of the plurality of layers comprises a peptide layer. 
     
     
         44 . The computer-readable medium of  claim 33  wherein one of the plurality of layers comprises a field-specific layer. 
     
     
         45 . The computer-readable medium of  claim 33  wherein one of the plurality of layers comprises an application layer. 
     
     
         46 . The computer-readable medium of  claim 33  wherein one of the plurality of layers comprises a user-specific layer. 
     
     
         47 . The computer-readable medium of  claim 30  wherein at least a portion of the information comprises medical records data. 
     
     
         48 . The computer-readable medium of  claim 31  wherein at least a portion of the information comprises gene expression data. 
     
     
         49 . The computer-readable medium of  claim 31  wherein at least a portion of the information comprises microarray data. 
     
     
         50 . The computer-readable medium of  claim 30  wherein at least a portion of the information comprises molecular pathways information. 
     
     
         51 . The computer-readable medium of  claim 30  wherein the information is contained within each said set of headers. 
     
     
         52 . The computer-readable medium 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. 
     
     
         53 . The computer-readable medium 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 stored within a second memory element. 
     
     
         54 . The computer-readable medium 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. 
     
     
         55 . The computer-readable medium of  claim 33  wherein a first of the plurality of layers comprises a DNA layer. 
     
     
         56 . The computer-readable medium of  claim 55  wherein the information associated with one header of the set of headers relating to the DNA layer comprises methylation pattern information. 
     
     
         57 . The computer-readable medium of  claim 55  wherein the information associated with one header of the set of headers relating to the DNA layer comprises chromosomal rearrangement information. 
     
     
         58 . The computer-readable medium of  claim 55  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. 
     
     
         59 . The computer-readable medium of  claim 55  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. 
     
     
         60 . The computer-readable medium of  claim 55  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. 
     
     
         61 . The computer-readable medium of  claim 55  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. 
     
     
         62 . The computer-readable medium of  claim 55  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. 
     
     
         63 . The computer-readable medium of  claim 55  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. 
     
     
         64 . The computer-readable medium of  claim 55  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. 
     
     
         65 . The computer-readable medium of  claim 55  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. 
     
     
         66 . The computer-readable medium of  claim 55  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. 
     
     
         67 . The computer-readable medium of  claim 30  wherein the information comprises one or more of medical, clinical, pharmaceutical, environmental and experimental data. 
     
     
         68 . The computer-readable medium of  claim 67  wherein the information further includes test results. 
     
     
         69 . The computer-readable medium 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 computer-readable medium for storing a data container having a data structure which facilitates processing of monomer sequence data in a data processing system, the medium comprising:
 a plurality of polymeric data units associated with the data container, each of the plurality of polymeric data units including:
 a payload containing a representation of at least a portion of a monomer sequence of a polymeric molecule, and 
 a set of headers associated with information relating to the at least a portion of the monomer sequence; 
   wherein the representation of at least a portion of a monomer sequence of ones of the plurality of polymeric data units may be packetized with the information of ones of the plurality of polymeric data units for use within the data processing system.   
     
     
         71 . The computer-readable medium 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 computer-readable medium for storing a data container having a data structure which facilitates processing of biological sequence data in a data processing system, the medium comprising:
 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 header, the first header 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 second header, the second header 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;   wherein the first segmented biological sequence data may be packetized with at least the first header and the second segmented biological sequence data may be packetized with at least the second header.   
     
     
         73 . The computer-readable medium of  claim 72  wherein the first type of organism comprises  homo sapiens.    
     
     
         74 . The computer-readable medium of  claim 73  wherein the second type of organism comprises bacteria. 
     
     
         75 . The computer-readable medium 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 computer-readable medium 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 computer-readable medium of  claim 72  wherein the first biological sequence data comprises genomic sequence data. 
     
     
         78 . A computer-readable medium for storing a data container having a data structure which facilitates processing of a biological data unit in a data processing system, the medium comprising:
 a representation of a DNA sequence comprised of a plurality of binary codes arranged in a sequence corresponding to a sequence of positions in the DNA sequence; and   a header field associated with information relating to the DNA sequence;   wherein each binary code included within a first group of the plurality of binary codes represents one of a plurality of nucleotide bases,   wherein each binary code included within a second group of the plurality of binary codes represents one of the plurality of nucleotide bases and at least one property associated with the one of the plurality of nucleotide bases;   wherein the representation of the DNA sequence may be packetized with the information for use within the data processing system.   
     
     
         79 . The computer-readable medium of  claim 78  wherein the at least one property relates to methylation. 
     
     
         80 . The computer-readable medium of  claim 79  wherein one binary code included within the second group of the plurality of binary codes represents methylated adenine. 
     
     
         81 . The computer-readable medium of  claim 79  wherein one binary code included within the second group of the plurality of binary codes represents methylated cytosine. 
     
     
         82 . The computer-readable medium of  claim 78  wherein the at least one property relates to an electrical charge. 
     
     
         83 . A computer-readable medium for storing a data container having a data structure which facilitates processing of a biological data unit in a data processing system, the medium comprising:
 a representation of a DNA sequence comprised of a plurality of binary codes arranged in a sequence corresponding to a sequence of positions in the DNA sequence; and   a header field associated with information relating to the DNA sequence;   wherein each binary code included within a first group of the plurality of binary codes represents one of a plurality of nucleotide bases,   wherein each binary code included within a second group of the plurality of binary codes represents a set of two or more of the plurality of nucleotide bases alternatively associated with one of the positions in the DNA sequence;   wherein the representation of the DNA sequence may be packetized with the information for use within the data processing system.   
     
     
         84 . The computer-readable medium of  claim 83  wherein the plurality of nucleotide bases comprise the nucleotide bases within the set consisting of cytosine, adenine, guanine, and thymine, and base analogs of the nucleotide bases with the set. 
     
     
         85 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of adenine and cytosine. 
     
     
         86 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of adenine and guanine. 
     
     
         87 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of adenine and thymine. 
     
     
         88 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of cytosine and guanine. 
     
     
         89 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of cytosine and thymine. 
     
     
         90 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of guanine and thymine. 
     
     
         91 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of adenine, cytosine and guanine. 
     
     
         92 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of adenine, cytosine and thymine. 
     
     
         93 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of adenine, guanine and thymine. 
     
     
         94 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of adenine, guanine and thymine. 
     
     
         95 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of cytosine, guanine and thymine. 
     
     
         96 . The computer-readable medium of  claim 84  wherein one binary code included within the second group of the plurality of binary codes represents the set of consisting of adenine, cytosine, guanine and thymine. 
     
     
         97 . The computer-readable medium of  claim 83  wherein each of the plurality of binary codes includes at least 4 bits. 
     
     
         98 . A computer-readable medium for storing a data container having a data structure which facilitates processing of sequence information in a data processing system, the medium comprising:
 a representation of a DNA sequence comprised of a plurality of binary codes wherein at least one of the plurality of binary codes represents at least one nucleotide base and other information associated with the DNA sequence; and   a header field associated with header information relating to the DNA sequence;   wherein the representation of the DNA sequence may be packetized with the header information for use within the data processing system.   
     
     
         99 . The computer-readable medium of  claim 98  wherein the other information comprises a property of the one nucleotide base. 
     
     
         100 . The computer-readable medium of  claim 98  wherein the other information identifies an additional nucleotide base, the at least one nucleotide base and the additional nucleotide base being alternatively associated with a position in the DNA sequence. 
     
     
         101 . The computer-readable medium of  claim 98  wherein the biological data unit further comprises at least one header relating to the representation of the DNA sequence. 
     
     
         102 . The computer-readable medium of  claim 101  wherein a value associated with the at least one header is indicative of a number of bits included within at least one of the plurality of binary codes. 
     
     
         103 . The computer-readable medium of  claim 101  wherein a header value associated with the at least one header is indicative of a type of the other information. 
     
     
         104 . The computer-readable medium of  claim 103  wherein the other information comprises a property of the one nucleotide base. 
     
     
         105 . The computer-readable medium of  claim 103  wherein the header value indicates that the property relates to methylation. 
     
     
         106 . The computer-readable medium of  claim 78  wherein the at least one property relates to a modification of the one of the plurality of nucleotide bases. 
     
     
         107 . A computer program product for facilitating operation of a data processing system including a data container having a data structure which accommodates polymeric sequence data, the computer program product comprising a computer-readable medium including codes for causing a computer to:
 receive 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, 
 at least one header associated with information relating to the segmented polymeric sequence data; and 
   store the plurality of polymeric data units within the data container wherein the segmented polymeric sequence data may be packetized with the information for use within the data processing system.   
     
     
         108 . A computer program product for facilitating operation of a data processing system including a data container having a data structure which accommodates polymeric sequence data, the computer program product comprising a computer-readable medium including codes for causing a computer to:
 receive DNA sequence data;   generate a representation of the DNA sequence data comprised of a plurality of binary codes arranged in a sequence corresponding to a sequence of positions in the DNA sequence data,   wherein each binary code included within a first group of the plurality of binary codes represents one of a plurality of nucleotide bases, and   wherein each binary code included within a second group of the plurality of binary codes represents one of the plurality of nucleotide bases and at least one property associated with the one of the plurality of nucleotide bases; and   store the representation of the DNA sequence data within the data container wherein the representation of the DNA sequence data may be packetized with header information associated with the DNA sequence data for use within the data processing system.