Method and Apparatus for Approximate Matching of DNA Sequences
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Abstract
A method and device are disclosed for an associative and approximate, analog or digital scanning of databases that allows for the asynchronous accessing of data from a mass storage medium. The invention includes providing dedicated analog and digital circuitry and decision logic at the mass storage medium level for determining a key identifying the data of interest, continuously comparing the key to a signal generated from a reading of the data from the mass storage medium with an approximate or exact matching circuit to determine a pattern match, determining a correlation value between the key and the data as it is read in a continuous fashion, and determining a match based upon a preselected threshold value for the correlation value. The pattern matching technique eliminates any need to compare data based on its intrinsic structure or value, and instead is based on an analog or digital pattern. The key and data may be either analog or digital. This device and method may be provided as part of a stand-alone computer system, embodied in a network attached storage device, or can otherwise be provided as part of a computer LAN or WAN.
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Citations
62 Claims
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1-37. -37. (canceled)
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38. A method for determining whether a DNA query sequence is an approximate match to a DNA sequence within a library of DNA sequences, the method comprising:
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streaming the DNA sequences of the library through programmable logic that has been loaded with a key, wherein the key corresponds to a DNA query sequence; and comparing the streaming DNA sequences with the key using the programmable logic to thereby identify any approximate matches that exist between the key and the streaming DNA sequences. - View Dependent Claims (39, 40, 41, 42, 43, 44, 45, 46, 47)
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48. An apparatus for determining whether a DNA query sequence is an approximate match to a DNA sequence that is stored by a mass storage medium as part of a library of DNA sequences, the apparatus comprising:
an approximate matching unit in communication with a mass storage medium, the approximate matching unit comprising programmable logic, the programmable logic being configured to (1) store a key, the key corresponding to a DNA query sequence, (2) receive a stream of DNA sequences from the mass storage medium, and (3) compare the received stream of DNA sequences with the key to thereby identify any approximate matches that exist between the key and the received DNA sequences. - View Dependent Claims (49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59)
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60. A method for determining whether a DNA query sequence is an approximate match to a DNA sequence within a library of DNA sequences, the method comprising:
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reading a plurality of DNA sequences from a mass storage medium as a stream of DNA sequences; correlating a sliding window of the stream with a key using programmable logic, wherein the key corresponds to a DNA query sequence; and determining whether an approximate match exists between the key and the window in response to the correlating step - View Dependent Claims (61, 62)
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Specification