Methods and systems for compressing and comparing genomic data

Abstract

Systems and methods are disclosed for compressing and comparing data such as genomic data. The disclosed systems and methods may include selecting a segment, creating a delta representation of the segment, the delta representation comprising a script, and storing the script. Furthermore, the disclosed systems and methods may include receiving a first script comprising a compressed version of a first segment and receiving a second script comprising a compressed version of a second segment. The disclosed systems and methods may further include comparing the first script to the second script and determining if the first segment matches the second segment based upon the comparison of the first script to the second script.

1 - 16 . (canceled) 
     
     
         17 . A method for comparing data, the method comprising:
 receiving a first script comprising a compressed version of a first segment;   receiving a second script comprising a compressed version of a second segment;   comparing the first script to the second script; and   determining if the first segment matches the second segments based upon the comparison of the first script to the second script.   
     
     
         18 - 28 . (canceled) 
     
     
         29 . A system for compressing data, the system comprising:
 a memory storage for maintaining a database; and   a processing unit coupled to the memory storage, wherein the processing unit is operative to
 select a segment; 
 create a delta representation of the segment, the delta representation comprising a script; and 
 store the script. 
   
     
     
         30 . The system of  claim 29 , wherein the processing unit being operative to select the segment further comprises the processing unit being operative to select the segment including genomic data. 
     
     
         31 - 33 . (canceled) 
     
     
         34 . The system of  claim 29 , wherein the processing unit being operative to create the delta representation further comprises the processing unit being operative to create the delta representation of the segment, the delta representation comprising a script comprising a compact symbolic representation. 
     
     
         35 . The system of  claim 29 , wherein the processing unit being operative to create the delta representation further comprises the processing unit being operative to
 select a reference sequence; and   align the reference sequence and the segment.   
     
     
         36 . The system of  claim 35 , wherein the processing unit being operative to select the reference sequence further comprises the processing unit being operative to select the reference sequence comprising a completed human genome. 
     
     
         37 . (canceled) 
     
     
         38 . The system of  claim 29 , wherein the processing unit being operative to create the delta representation further comprises the processing unit being operative to create the delta representation of the segment, the delta representation comprising the script configured to indicate at least one operation. 
     
     
         39 . The system of  claim 29 , wherein the processing unit being operative to create the delta representation further comprises the processing unit being operative to create the delta representation of the segment, the delta representation comprising the script configured to indicate at least one operation comprising one of insert, delete, substitute, and copy. 
     
     
         40 . The system of  claim 29 , wherein the processing unit being operative to create the delta representation further comprises the processing unit being operative to create the delta representation of the segment, the delta representation comprising the script comprising at least one symbol, the at least one symbol being configured to be looked-up in a dictionary to Indicate a feature associated with the at least one symbol. 
     
     
         41 . The system of  claim 29 , wherein the processing unit being operative to create the delta representation further comprises the processing unit being operative to create the delta representation of the segment, the delta representation comprising the script comprising at least one symbol, the at least one symbol being configured to be looked-up in a dictionary to indicate an operation associated with the at least one symbol, the operation comprising one of insert, delete, substitute, and copy. 
     
     
         42 . (canceled) 
     
     
         43 . The system of  claim 29 , wherein the processing unit being operative to store the script further comprises the processing unit being operative to store the script in a relational database configured to include a segment table having a one-to-many relationship with a variant table. 
     
     
         44 . (canceled) 
     
     
         45 . A system for comparing data, the system comprising:
 a memory storage for maintaining a database; and   a processing unit coupled to the memory storage, wherein the processing unit is operative to
 receive a first script comprising a compressed version of a first segment; 
 receive a second script comprising a compressed version of a second segment; 
 compare the first script to the second script; and 
 determine if the first segment matches the second segments based upon the comparison of the first script to the second script. 
   
     
     
         46 . The system of  claim 45 , wherein at least one of the first segment and the second segment includes genomic data. 
     
     
         47 - 48 . (canceled) 
     
     
         49 . The system of  claim 45 , wherein at least one of the first script and the second script comprises a compact symbolic representation. 
     
     
         50 . The system of  claim 45 , wherein at least one of the first script and the second script comprises a delta representation. 
     
     
         51 . The system of  claim 45 , wherein the delta representation was created with a reference sequence comprising a completed human genome. 
     
     
         52 . (canceled) 
     
     
         53 . The system of  claim 45 , wherein at least one of the first script and the second script is configured to indicate at least one operation. 
     
     
         54 . The system of  claim 45 , wherein at least one of the first script and the second script is configured to indicate at least one operation comprising one of insert, delete, substitute, and copy. 
     
     
         55 . The system of  claim 45 , wherein at least one of the first script and the second script comprises at least one symbol, the at least one symbol being configured to be looked-up in a dictionary to indicate a feature associated with the at least one symbol. 
     
     
         56 . The system of  claim 45 , wherein at least one of the first script and the second script comprises at least one symbol, the at least one symbol being configured to be looked-up in a dictionary to indicate an operation associated with the at least one symbol, the operation comprising one of insert, delete, substitute, and copy. 
     
     
         57 - 84 . (canceled)