System and method for pattern recognition in sequential data
First Claim
1. A method of comparing sequential data, comprising:
- (a) providing a target sequence and a query sequence, wherein each sequence is encoded as a set of at least two n-bit binary strings wherein each bit of each binary string is aligned with the corresponding bit of the other binary string, thereby identifying n groups of aligned bits, wherein each group of aligned bits defines an identity of a component of the sequence;
(b) determining, by an ordered comparison of the binary strings of the query sequence with corresponding binary strings of the target sequence, a match between the query sequence and the target sequence; and
(c) generating an indication of a match of the target and query sequences based on the ordered comparison.
1 Assignment
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Accused Products
Abstract
The present invention is based on the encoding of sequential data or sequences in a novel manner that permits efficient storage and processing of sequential data, as well as methods for searching sequences or databases of sequences. The methods and systems of the current invention may be adapted broadly to various fields of application and to a variety of sequences types. For example, the current invention has broad application including to the fields of bioinformatics, molecular biology, pharmacogenomics, phonetic sequences, lexicographic sequences, signal analysis, game playing, law enforcement, biometrics, medical diagnosis, equipment maintenance and micro-array data analysis.
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Citations
184 Claims
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1. A method of comparing sequential data, comprising:
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(a) providing a target sequence and a query sequence, wherein each sequence is encoded as a set of at least two n-bit binary strings wherein each bit of each binary string is aligned with the corresponding bit of the other binary string, thereby identifying n groups of aligned bits, wherein each group of aligned bits defines an identity of a component of the sequence;
(b) determining, by an ordered comparison of the binary strings of the query sequence with corresponding binary strings of the target sequence, a match between the query sequence and the target sequence; and
(c) generating an indication of a match of the target and query sequences based on the ordered comparison. - View Dependent Claims (2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 18, 22, 23, 24, 25, 35, 36, 40, 48, 49, 55)
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8. (canceled)
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17. (canceled)
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19-21. -21. (canceled)
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26-34. -34. (canceled)
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37-39. -39. (canceled)
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41-47. -47. (canceled)
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50-54. -54. (canceled)
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56. A method of identifying matching biomolecule sequence data, comprising:
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(a) providing a database comprising a target biomolecule sequence and a query biomolecule sequence, wherein each sequence is encoded as a set of at least two n-bit binary strings wherein each bit of each binary string is aligned with the corresponding bit of the other binary string, thereby identifying n groups of aligned bits, wherein each group of aligned bits defines an identity of a component of the sequence;
(b) determining, by an ordered comparison of the binary strings of the query biomolecule sequence with corresponding binary strings of the target biomolecule sequence, a match between the query sequence and the target sequence; and
(c) generating an indication of a match of the target and query biomolecule sequences based on the ordered comparison. - View Dependent Claims (57, 58, 59, 60, 63, 66, 67)
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61-62. -62. (canceled)
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64-65. -65. (canceled)
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68-69. -69. (canceled)
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70. A computer system, comprising:
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(a) a searchable database of sequences, wherein each sequence is encoded as a set of at least two n-bit binary strings wherein each bit of each binary string is aligned with the corresponding bit of the other binary string, thereby identifying n groups of aligned bits, wherein each group of aligned bits defines an identity of a component of the sequence; and
(b) a user interface capable of receiving a selection of at least two sequences for determining, by an ordered comparison of corresponding binary strings of the selected sequences, a match between the selected sequences, and displaying the results of the determination.
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71-138. -138. (canceled)
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139. A method of identifying a region of interest in a sequence, comprising:
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(a) providing a query sequence representing a region of interest and a target sequence, wherein each sequence is encoded as a set of at least two n-bit binary strings wherein each bit of each binary string is aligned with the corresponding bit of the other binary string, thereby identifying n groups of aligned bits, wherein each group of aligned bits defines an identity of a component of the sequence;
(b) determining, by an ordered comparison of the binary strings of the query sequence with corresponding binary strings of the target sequence, a match between the query sequence and the target sequence; and
(c) generating an indication of a match of the target and query sequences based on the ordered comparison.
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140. The method of 139, further comprising displaying the results of the comparison.
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141. The method of 139, wherein the sequences comprise nucleotide sequences, amino acid sequences, phonetic sequences, speech pattern sequences, signal analysis sequences, graphic image sequence data, law enforcement related sequence data, or data related to mechanical equipment status.
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142-143. -143. (canceled)
- 144. A computer-readable data storage medium comprising a plurality of digitally-encoded sequences, wherein each sequence is encoded as a set of at least two n-bit binary strings wherein each bit of each binary string is aligned with the corresponding bit of the other binary string, thereby identifying n groups of aligned bits, wherein each group of aligned bits defines an identity of a component of the sequence.
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145. (canceled)
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148-160. -160. (canceled)
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162-167. -167. (canceled)
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169-183. -183. (canceled)
Specification