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US 8,937,564 B2Granted
System, method and non-transitory computer readable medium for compressing genetic information
AssigneeInfinidat Ltd.
InventorsDan Aloni, Jacob Brodio, Kariel Sandler, Cyril Plisko, Alexander Goldberg
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Abstract
A method for compressing information by a computerized system, the method may include receiving a mixture of DNA data and additional information; and compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data.
Claims32
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA deoxyribonucleic acid data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- selecting, out of multiple predefined codeword dictionaries, the predefined codeword dictionary used for compressing the DNA data based upon an expected resemblance between the DNA data and the reference DNA data.
1 more element
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- selecting out of multiple predefined codeword dictionaries the predefined codeword dictionary, wherein the selecting comprises finding the predefined codeword dictionary that is expected to provide a best match to the DNA data.
1 more element
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- generating location information indicative of a location of DNA data elements and additional information elements within the mixture.
1 more element
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- extracting the DNA data from the mixture by searching for DNA fragment strings.
1 more element
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- and compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- wherein the mixture comprises multiple information strings;
- and wherein the method comprises concatenating DNA fragment strings from the multiple information strings to provide the DNA data.
1 more element
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- and compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- wherein the DNA data relates to a first species and the reference DNA data relates to a second species.
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- and compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- wherein the compressing comprises finding a certain DNA fragment string that does not match any codeword of the predefined codeword dictionary;
- and calculating a certain new codeword representative of the certain DNA fragment string.
1 more element
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- replacing the predefined codeword dictionary by another predefined codeword dictionary;
- and storing at a storage system the predefined codeword dictionary and the other predefined codeword dictionary.
2 more elements
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- comparing compression performances of a plurality of predefined codeword dictionaries, and determining to replace the predefined codeword dictionary by another predefined codeword dictionary if it is determined that the other predefined dictionary exhibits better compression performance than the predefined codeword dictionary.
1 more element
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- comparing compression ratios obtained by applying different predefined codeword dictionaries;
- and selecting a predefined codeword dictionary that exhibits a best compression ratio.
2 more elements
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- storing at a storage system the compressed DNA data, the additional information and location information indicative of a location of DNA data elements and additional information elements within the mixture.
1 more element
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- receiving a request to retrieve the mixture;
- decrypting the compressed DNA data to provide the DNA data;
- and reconstructing the mixture by using location information indicative of a location of DNA data elements and additional information elements within the mixture.
2 more elements
A method for compressing information by a computerized system, the method comprises:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- building the predefined codeword dictionary by traversing the reference DNA data, each time extending a lookup table that forms the predefined codeword dictionary, adding codewords of variable length.
1 more element
A non-transitory computer readable medium, that stores instructions for:
- receiving a mixture of DNA data and additional information;
- compressing the DNA data to provide compressed DNA data, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and
- selecting, out of multiple predefined codeword dictionaries, the predefined codeword dictionary used for compressing the DNA data based upon an expected resemblance between the DNA data and the reference DNA data.
1 more element
A computerized system, comprising:
- an communication module arranged to receive a mixture of DNA data and additional information;
- and
- a genetic data processor arranged to (a) compress the DNA data to provide compressed DNA, wherein the compressing comprises encoding the DNA data by using a predefined codeword dictionary that was constructed based upon reference DNA data;
- and (b) selecting, out of multiple predefined codeword dictionaries, the predefined codeword dictionary used for compressing the DNA data based upon an expected resemblance between the DNA data and the reference DNA data.
1 more element
Dependencies are inferred from the claim text.