DETAILED ACTION Comments The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis ( i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status. Claims 1-20 are pending and examined in the instant Office action. Claim Interpretation The following is a quotation of 35 U.S.C. 112(f): (f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph: An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitation(s) is/are: “information unit” in claims 1-20. Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. Pages 4-5 of the specification disclose that the information unit can be data or hardware associated with the CPU. Claim Rejections - 35 USC § 112(b) - Indefiniteness The following is a quotation of 35 U.S.C. 112(b): (b ) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention. The following is a quotation of 35 U.S.C. 112 (pre-AIA), second paragraph: The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the appl icant regards as his invention. Claims 1-10 and 12-20 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. The claims recite use of the shortest common supersequence (SCS). It is unclear as to relative to what size the common supersequence is the shortest. The claims also recite use of the longest common subsequences (LCS) and longest traces of the cluster. It is unclear as to relative to what size the common subsequence and the longest traces of the cluster are the longest. For the purpose of examination, any common subsequence is interpreted to be either the SCS or the LCS, and any trace s of a cluster are interpreted to be the longest traces of the cluster. Claim 11 is NOT rejected under this statute because claim 11 limits the longest traces of a cluster to be about one fifth of the cluster with the longest traces. Claim 15 is a non-transitory computer readable medium claim dependent from method claim 3. For the purpose of examination, it is interpreted that claim 15 depends from claim 14. Claim 17 is a non-transitory computer readable medium claim dependent from method claim 13. For the purpose of examination, it is interpreted that claim 17 depends from claim 14. Claim 20 is a non-transitory computer readable medium claim dependent from method claim 13. For the purpose of examination, it is interpreted that claim 20 depends from claim 14. Claim Rejections - 35 USC § 101 35 U.S.C. 101 reads as follows: Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title. Claim(s) 1-20 is/are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. Claims 1-13 are drawn to methods, and claims 14-20 are drawn to non-transitory computer readable media. In accordance with MPEP § 2106, claims found to recite statutory subject matter ( Step 1 : YES ) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon ( Step 2A, Prong 1 ). In the instant application, the claims recite the following limitations that equate to an abstract idea: The independent claims recite the mental step of applying processing operations on r-tuples related to the traces, where r is smaller than a number of traces of the cluster. The independent claims recite the mental step of calculating a length of an SCS of the r-tuples. Claims 2 and 15 recite the mental step of searching for a maximum likelihood SCS. Claims 3 and 16 recite the mathematical limitation of returning a SCS that minimizes a sum Levenshtein distances of all the traces of the cluster. Claims 4 and 17 recite the mental step of repeating the processing operations for different values of r. Claims 5 and 18 recite the mental step of constraining r to not exceed 10. Claims 6 and 19 recite the mental step of constraining r to only comprise a few values. Claims 7 and 20 recite the mental step of calculating LCSs. Claim 8 recites the mental step of constraining the data to be based on the size of the cluster. Claim 9 recites the mathematical limitation of an estimate of an error probability of the cluster using an average length of the traces. Claim 10 recites the mental step of applying processing operations only to the longest traces of the cluster. Claim 11 recites the mental step of constraining the longest traces to be about one-fifth of the traces in the cluster. Claim 12 recites a mathematical limitation of calculating a distance between the traces of the cluster. Claim 13 recites the mental step of constraining the distance to be a k- mer distance. These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claim(s) 1-20 recite(s) an abstract idea/law of nature/natural phenomenon ( Step 2A, Prong 1 : YES ). Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not ( Step 2A, Prong 2 ). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to a ffect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or mere instructions to apply the recited judicial exception via a generic treatment. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. As such, claims 1-20 is/are directed to an abstract idea/law of nature/natural phenomenon ( Step 2A, Prong 2 : NO ). Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself ( Step 2B ). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment. As discussed above, there are no additional limitations to indicate that the claimed analysis engine requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself ( Step 2B : No ). As such, claims 1-20 is/are not patent eligible. Claim Rejections - 35 USC § 102 The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action: A person shall be entitled to a patent unless – (a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale , or otherwise available to the public before the effective filing date of the claimed invention. (a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention. Claim(s) 1-10 and 12-20 is/are rejected under 35 U.S.C. 102 (a)(2) as being anticipated by Makarychev [US PGPUB 2019/0377851 A1; on attached 892 form] . Claim 1 is drawn to a method for estimating an information unit represented by a cluster of traces that are noisy copies of a synthesized strand. The method comprises estimating the information unit by applying processing operations on r-tuples related to the traces, where r is smaller that a number of traces of the cluster. Processing operations applied on at least some of the r-tuples comprise calculating a length of SCS of the r-tuples. Claim 14 is drawn to similar subject matter as claim 1, except claim 14 is drawn to a non-transitory computer readable medium. The document of Makarychev studies efficient payload extraction from polynucleotide sequence reads [title]. Paragraph 49 of Makarychev teaches the computer limitations of the claims. Paragraphs 4-5 of Makarychev teach synthesizing and performing processing operations on a combinatorial number of noisy copies of DNA strands (i.e. traces). Paragraphs 98-99 of Makarychev teach k- mers (i.e. r-tuples) within the sequences with the size of 3 (i.e. r = 3). Three (i.e. paragraphs 98-99 of Makarychev ) is less than the combinatorial number of traces taught in paragraphs 4-5 of Makarychev . With regard to claims 2-3 and 15-16, paragraphs 77-78 of Makarychev teaches either finding a maximum likelihood SCS or an SCS that minimizes a sum of Levenshtein distances of all the traces of the cluster. With regard to claims 4-6 and 17-19, paragraph 65 of Makarychev exemplifies k (i.e. r) equaling 1, 2, 3, 4, 5 (I.e. a few values that are less than 10). With regard to claims 7 and 20, paragraphs 98-99 of Makarychev teach k- mers (i.e. r-tuples) within the sequences with the size of 3 (i.e. r = 3). With regard to claim 8, Figure 1 of Makarychev illustrates the information unit is based on the size of the data. With regard to claims 9-10 and 12-13, paragraphs 77-78 of Makarychev teaches that the data is based on error probabilities in the cluster measured using Levenshtein distances between traces in the cluster and comprises conducting calculation on the longest traces of the cluster. Paragraphs 65 and 98-99 of Makarychev teach k- mers distances within the sequences. Related Prior Art The document of Magner et al. [IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, 2016, pages 1-18; on attached 892 form] studies fundamental bounds for sequence reconstruction from nanopore sequencers [title]. Figure 1 of Magner et al. illustrates an overview of the procedures wherein traces are compared to series of identical bases to detect insertion and deletion errors. The document of Levenshtein [IEEE Transactions on Information Theory , 2001; on attached 892 form] outlines the mathematical basis for reconstruction of sequences within a threshold distance of the original sequence. Conclusion No claim is allowed. Claim 11 is free of the prior art because the prior art does not teach an analogous algorithm wherein about one-fifth of the traces in the cluster are classified as the longest traces within the cluster. Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Russell Negin, whose telephone number is (571) 272-1083. This Examiner can normally be reached from Monday through Thursday from 8 am to 3 pm and variable hours on Fridays. If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s Supervisor, Larry Riggs, Supervisory Patent Examiner, can be reached at (571) 270-3062. /RUSSELL S NEGIN/ Primary Examiner, Art Unit 1686 14 December 2025