Methods and systems for processing genomic data

Abstract

Methods and systems for processing biological sequence data, such as genomic data, are disclosed. In one implementation, a set of biological sequences, such as DNA sequences, may be evaluated and one or more reference sequences may be determined or selected based on the set of biological sequences, which may include iterative determination or selection. The set of biological sequences may be compressed using the one or more reference sequences. Processing may include generating delta representations associated with the biological sequences, as well as generating dictionary information, which may be used for further compression. Metadata may be included in the compressed data. The compressed data may be stored in a compressed data file, which may be in a compressed genomic database or other data storage medium.

1 . A computer-implemented method of compressing a plurality of data sequences for use in a system including at least a processor and a memory storing a database of biological sequence data, the method comprising:
 determining, based upon comparison of the plurality of data sequences prior to compression of the plurality of data sequences, a reference sequence wherein the reference sequence includes data from the plurality of data sequences;   processing the plurality of data sequences relative to the reference sequence in order to determine differences between the plurality of data sequences and the reference sequence;   creating, using the reference sequence and based upon the differences, a plurality of first delta representations of the plurality of data sequences wherein the creating includes specifying, for each of the differences in ones of the plurality of first delta representations, a corresponding position in the modified reference sequence, an operation, and a value associated with the operation;   defining a modified reference sequence;   generating, using the modified reference sequence, a plurality of second delta representations of the plurality of data sequences;   storing the plurality of first delta representations and the plurality of second delta representations in the database, thereby representing the plurality of first delta representations in a compressed format and conserving resources of the memory; and   transmitting at least one of the plurality of first delta representations and one of the second plurality of representations.   
     
     
         2 . The computer-implemented method of  claim 1  further including evaluating the plurality of first delta representations wherein the defining includes generating the modified reference sequence by modifying the reference sequence based upon the evaluating. 
     
     
         3 . The computer-implemented method of  claim 1 , further comprising replacing a portion of one of the plurality of first delta representations with address information associated with a dictionary structure, the portion of the first delta representation being stored within the dictionary structure. 
     
     
         4 . The computer-implemented method of  claim 2 , further comprising replacing a portion of one of the plurality of second delta representations with address information associated with a dictionary structure, the portion of the second delta representation being stored within the dictionary structure. 
     
     
         5 . The computer-implemented method of  claim 2 , wherein the defining is further based upon one or more characteristics of the plurality of first delta representations, wherein the one or more characteristics relate to a set of delta values associated with one or more predefined regions of the plurality of data sequences. 
     
     
         6 . The computer-implemented method of  claim 5 , wherein the plurality of sequences comprise DNA sequences and wherein the one or more predefined regions are known to be associated with one or more disease conditions. 
     
     
         7 . The computer-implemented method of  claim 5 , wherein the plurality of sequences comprise DNA sequences and wherein the one or more predefined regions are predicted to be associated with one or more disease conditions. 
     
     
         8 . The computer-implemented method of  claim 5 , wherein the plurality of sequences comprise DNA sequences and wherein the one or more predefined regions are not known to be associated with a disease condition. 
     
     
         9 . The computer-implemented method of  claim 1 , wherein the defining includes:
 identifying at least one sequence segment common to plural ones of the plurality of first delta representations; and   modifying the reference sequence in accordance with the at least one sequence segment.   
     
     
         10 . The computer-implemented method of  claim 9 , wherein the plurality of data sequences comprise DNA data sequences and wherein the at least one sequence segment comprises a mutation. 
     
     
         11 . The computer-implemented method of  claim 1 , wherein the plurality of data sequences are stored within a database, the database further including embedded data associated with segments of the plurality of data sequences. 
     
     
         12 . The computer-implemented method of  claim 11 , wherein the plurality of data sequences comprise DNA data sequences and wherein the segments comprise mutations. 
     
     
         13 . The computer-implemented method of  claim 11 , further including replacing at least a portion of the embedded data with address information associated with a dictionary structure, the at least a portion of the embedded data being stored within the dictionary structure. 
     
     
         14 . The computer-implemented method of  claim 13 , wherein the plurality of data sequences comprise DNA data sequences and wherein the embedded data comprises correlative information relating to mutations within the DNA data sequences. 
     
     
         15 . The computer-implemented method of  claim 14 , wherein the correlative information includes pharmacological information. 
     
     
         16 . The computer-implemented method of  claim 14 , wherein the correlative information includes clinical result information. 
     
     
         17 . The computer-implemented method of  claim 1 , wherein the operation corresponding to one of the differences comprises substitution. 
     
     
         18 . The computer-implemented method of  claim 1 , wherein the operation corresponding to one of the differences comprises insertion. 
     
     
         19 . (canceled) 
     
     
         20 . A computer program product comprising a non-transitory computer readable medium including codes for causing a computer to:
 determine, based upon comparison of a plurality of data sequences to be compressed, a reference sequence wherein the reference sequence includes data from the plurality of data sequences;   process the plurality of data sequences relative to the reference sequence in order to determine differences between the plurality of data sequences and the reference sequence;   create, using the reference sequence and based upon the differences, a plurality of first delta representations of the plurality of data sequences wherein for each of the differences, ones of the plurality of delta representations specify a corresponding position in the modified reference sequence, an operation, and a value associated with the operation;   define a modified reference sequence by modifying the reference sequence;   generate, using the modified reference sequence, a plurality of second delta representations of the plurality of data sequences;   store at least one of the plurality of first delta representations and the plurality of second delta representations in a database contained within a memory, thereby representing the plurality of first delta representations and the plurality of second delta representations in a compressed format and conserving resources of the memory; and   transmit at least one of the plurality of first delta representations and the plurality of second delta representations from the memory.   
     
     
         21 . A computer-implemented method for compressing sequence data in a system including at least a processor and a memory containing a database, the method comprising:
 determining, based upon comparison of a plurality of data sequences prior to compression of the plurality of data sequences, a reference sequence wherein the reference sequence includes data from the plurality of data sequences;   processing the sequence data relative to the reference sequence wherein the processing includes determining differences between the sequence data and the reference sequence;   receiving metadata relating to the sequence data;   generating, based upon the processing, a first delta representation of the sequence data wherein the delta representation includes compressed sequence data representative of the sequence data and embedded data representative of one or more characteristics of the sequence data wherein the embedded data includes the metadata and wherein the generating includes specifying, for each of the differences, a corresponding position in the reference sequence, an operation, and a value associated with the operation;   defining a modified reference sequence by modifying the reference sequence;   generating, using the modified reference sequence, a second delta representation of the sequence data;   storing the first delta representation and the second delta representation in a database, thereby representing the sequence data in a compressed format and conserving resources of the processor and the memory; and   generating a display on a display device using at least one the first delta representation and the second delta representation.   
     
     
         22 - 55 . (canceled)