CTNF 18/049,506 CTNF 96576 DETAILED ACTION Notice of Pre-AIA or AIA Status 07-03-aia AIA 15-10-aia The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA. 07-06 AIA 15-10-15 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 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. Election/Restrictions Applicant’s election without traverse of Group I, claims 1-10, in the reply filed on May 13 2026 is acknowledged. Nonelected claims 11-21 were canceled in Applicant’s reply. Claim Status Claims 1-10 are pending. Claims 11-21 are canceled. Claims 1 and 6-7 are objected to. Claims 1-10 are rejected. Priority The instant Application was filed Oct 25 2022 and does not claim the benefit of an earlier filed application. Information Disclosure Statement The information disclosure statement (IDS) filed on May 10 2024 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS document is included with this Office Action. Drawings The Drawings submitted Oct 25 2022 are accepted. Nucleotide and/or Amino Acid Sequence Disclosures REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES Items 1) and 2) provide general guidance related to requirements for sequence disclosures. 37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted: In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying: the name of the ASCII text file; ii) the date of creation; and iii) the size of the ASCII text file in bytes; In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying: the name of the ASCII text file; the date of creation; and the size of the ASCII text file in bytes; In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended). When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824. If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical. If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical. The specification includes sequences which fall within the definitions of 37 CFR 1.821(a) at least in FIG. 4-5, but does not include a sequence listing with SEQ IDs. Specific deficiencies and the required response to this Office Action are as follows: A. Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”. Required response - Applicant must provide: A "Sequence Listing" part of the disclosure; together with An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2) ; A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3). If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide: A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of: A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); A copy of the amended specification without markings (clean version); and A statement that the substitute specification contains no new matter. If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide: A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and A statement according to item 2) a) or b) above. B. Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because the application does not contain a statement that the CRF is identical to the "Sequence Listing" part of the disclosure, as described above in item 1), as required by 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii). Required response - Applicant must provide such statement. C. Specific deficiency - This application contains a “Sequence Listing as a PDF file (37 CFR 1.821(c)(2)) or as physical sheets of paper (37 CFR 1.821(c)(3)), but fails to comply with the requirements of 37 CFR 1.821 - 1.825 because a copy of the "Sequence Listing" in computer readable form (CRF) has not been submitted as required by 37 CFR 1.821(e)(1)(i) or 1.821(e)(2)(i) as indicated in item 2) above. Required response - Applicant must provide: A new CRF of the “Sequence Listing” in accordance with 37 CFR 1.821(e)(1)(i) or 1.821(e)(2)(i) and A statement that the content of the CRF is identical of the “Sequence Listing” part of the disclosure, submitted as a PDF file (37 CFR 1.821(c)(2)) or on physical sheets of paper (37 CFR 1.821(c)(3)), as required by 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii). D. Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Required response – Applicant must provide: A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of: A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); A copy of the amended specification without markings (clean version); and A statement that the substitute specification contains no new matter. E. Specific deficiency – Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings. Required response – Applicant must provide: Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers; AND/OR A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of: A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); A copy of the amended specification without markings (clean version); and A statement that the substitute specification contains no new matter. F. Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above. Required response – Applicant must provide: A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of: A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version); A copy of the amended specification without markings (clean version); and A statement that the substitute specification contains no new matter. Claim Objections The claims are objected to for the following informalities: Claim 1 , line 4, recites “of the plane of the plane”, which should be amended to remove one of the recitations of “of the plane”. Claim 7 , second limitation, is similarly objected to for “of the second plane of the second plane”. Claim 6 recites “wherein a number of plurality of values”, which should be amended to recite “wherein a number of the plurality of values”. Claim Rejections - 35 USC § 101 The claims are found to be patent eligible because they are directed to a method comprising storing nucleotides of a genetic sequence in a specific manner in an associative processing memory device comprising memory cells, which provides a result of a comparison between the stored sequence and a second sequence. The claims therefore recite a device which is a particular machine at Step 2A, Prong 2, for performing the judicial exception of “comparing” sequences, which provides a practical application. Claim Rejections - 35 USC § 102 07-07-aia AIA 07-07 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 – 07-08-aia AIA (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. 07-12-aia AIA (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. 07-15 AIA Claim s 1-2 and 5-10 are rejected under 35 U.S.C. 102( a)(1 ) as being anticipated by Angizi et al. (Proceedings of the 56th Annual Design Automation Conference, 2019 , p. 1-6; newly cited) . Claim 1 discloses a method comprising: storing, in a first column of a plane of an associative processing memory device (APM), a first genetic sequence, wherein individual rows of a plurality of rows in the first column store data corresponding to nucleotides of the first genetic sequence; Angizi discloses an energy-efficient and parallel Processing-in-Memory accelerator (AlignS) to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm (abstract). Angizi teaches that AlignS harnesses SOT-MRAM as computational memory ( i.e. , an associative processing memory device ) (abstract). Angizi teaches that the main memory rank is a set of MRAM chips, each divided into multiple Banks, each bank consisting of multiple memory matrices (mats), each mat consisting of multiple computation memory sub-arrays ( i.e. , plane ) (p. 2-3, section 2 ALIGNS ARCHITECTURE; Figure 1). Angizi teaches that each SOT-MRAM cell is located in computational sub- arrays , where Angizi also refers to the cells as memory cells (p. 2, col. 1, par. 3 through col. 2, par. 1; Figure 1b). Angizi teaches and illustrates the memory cells being arranged in a plurality of columns and rows (p. 2, col. 2, par. 2; Figure 1b). Angizi teaches pre-computing tables of a reference genome which are saved into memory arrays (p. 3, col. 2, par. 2; p. 2, col. 2, par. 2). Angizi teaches constructing a BW matrix by circulating the string of nucleotide sequences and then lexicographically sorting them, thereby providing a suffix array of the reference genome (p. 3, col. 2, par. 1; Figure 4). Angizi teaches storing the BWT, Marker Table, and Suffix Array in the memory cells of the sub-array, where individual rows are illustrated to store the sequences of the BWT of the reference sequence ( i.e. , data corresponding to nucleotides of a first genetic sequence ) (p. 3, col. 2, par. 2; p. 4, col. 2, par. 2; Figures 4-6(a)). storing, in a subsequent plurality of columns of the plane of the plane, a corresponding plurality of permutations of the first genetic sequence; Angizi teaches and illustrates an example of generating the BW matrix of the sequence ATTCG, where the first row of the BW matrix holds the sequence ATTCG ( i.e. , a first row of the plurality of columns stores data corresponding to the first genetic sequence ), and each subsequent row and column holds a sorted permutation of the circulated string of the reference nucleotide sequence (p. 3, col. 2, par. 1; Figure 4). As Angizi teaches storing the BWT and the Suffix Array in the memory cells of the sub-array (p. 3, col. 2, par. 2; Figures 4-6(a)), it is considered that Angizi fairly teaches the instant limitation. comparing, in parallel, a second genetic sequence to the first genetic sequence and the plurality of permutations of the first genetic sequence; and providing a result for the plane based, at least in part, on the comparing. Angizi teaches that the computation sub-array of AlignS is optimized to perform ( i.e. , configured to ) two bulk bit-wise in-memory logic operations between the operands located in the same bit-line (p. 2, col. 2, par. 2 through p. 3, col. 1, par. 2; Figure 1(b-c)). Angizi teaches a read searching operation ( i.e. , a result for the plane ) to compare reads with the stored BW matrix of the reference sequence in the sub-array in a parallel manner (p. 4, col. 1, par. 2 and col. 2, par. 3 through p. 5, col. 1, par. 1; Figures 5 and 7). Regarding claim 2 , Angizi teaches claim 1 as described above. Claim 2 further adds generating the plurality of permutations by shifting the first genetic sequence by one nucleotide per column for each one of the subsequent plurality of columns. Angizi teaches that the BW matrix is constructed by circulating ( i.e. , shifted permutations ) the string of nucleotide sequences, where the BWT is a permutation of the characters of the string (p. 3, col. 2, par. 1; Figure 4). Regarding claim 5 , Angizi teaches claim 1 as described above. Claim 5 further adds comparing, in parallel, a third genetic sequence to the first genetic sequence and the plurality of permutations of the first genetic sequence; and providing a second result for the plane based, at least in part, on the comparing. Angizi teaches a read searching operation ( i.e. , a result for the plane ) to compare reads with the stored BW matrix of the reference sequence in the sub-array in a parallel manner, (p. 4, col. 1, par. 2 and col. 2, par. 3 through p. 5, col. 1, par. 1; Figures 5 and 7). As Angizi teaches comparing multiple reads, and gives an example of a current input nucleotide (p. 4, col. 2, par. 3), it is considered that Angizi fairly teaches comparing a third genetic sequence in parallel to the stored permutations of the first genetic sequence and providing a second result for the plane as instantly claimed. Regarding claim 6 , Angizi teaches claim 1 as described above. Claim 6 further adds that providing the result comprises providing a plurality of values, wherein a number of plurality of values is equal to a number of the first column and the subsequent plurality of columns. Angizi teaches an XNOR_Match procedure to locate input nucleotide T in a sub-array storing the reference sequence (p. 4, col. 2, par. 3 through p. 5, col. 1, par. 1), where the output “count_match” is illustrated as a row of values for each nucleotide stored in the columns and rows of the sub-array (Figure 7). Regarding claim 7 , Angizi teaches claim 1 as described above. Claim 7 further adds storing, in a second column of a second plane, a third genetic sequence, wherein individual rows of a second plurality of rows in the second column store data corresponding to nucleotides of the third genetic sequence; and storing, in a second subsequent plurality of columns of the second plane of the second plane, a corresponding plurality of permutations of the third genetic sequence. Angizi teaches that in order to enable fast memory access and parallel in-memory computing, the data in BWT, Marker Table, and Suffix Array have to be reconstructed and saved into different memory arrays, banks, and chips (p. 3, col. 1, par. 2; p. 4, col. 1, par. 3 through p. 5, col. 1, par. 1; Figure 7), which reads on storing a third genetic sequence and its permutations in a second column of a second plane as instantly claimed. Regarding claim 8 , Angizi teaches claims 1 and 7 as described above. Claim 8 further adds that the first genetic sequence and the third genetic sequence are corresponding portions of a plurality of portions of a reference sequence. Angizi teaches that in order to enable fast memory access and parallel in-memory computing, the data in BWT, Marker Table, and Suffix Array have to be reconstructed and saved into different memory arrays, banks, and chips (p. 3, col. 1, par. 2; p. 4, col. 1, par. 3 through p. 5, col. 1, par. 1; Figure 7), which reads on the first and third genetic sequence being corresponding portions of a plurality of portions of a reference sequence. Regarding claim 9 , Angizi teaches claims 1 and 7-8 as described above. Claim 9 further adds that the first genetic sequence and the third genetic sequence overlap by at least one nucleotide. Angizi teaches that in order to enable fast memory access and parallel in-memory computing, the data in BWT, Marker Table, and Suffix Array have to be reconstructed and saved into different memory arrays, banks, and chips (p. 3, col. 1, par. 2; p. 4, col. 1, par. 3 through p. 5, col. 1, par. 1; Figure 7). It is considered that as Angizi teaches distributing the storage of the BWT, Marker Table, and Suffix Array across memory arrays, and as Angizi teaches that the BWT, Marker Table, and Suffix Array are generated from a BW matrix of a circulated and sorted string of nucleotide sequences (p. 3, col. 2, par. 1; Figure 4), it is considered that some of those distributed BWT, Marker Table, and Suffix Array would overlap by at least one nucleotide as instantly claimed. Regarding claim 10 , Angizi teaches claims 1 and 7 as described above. Claim 10 further adds that the plane and the second plane are located on different tiles of the APM device, the method further comprising: comparing, in parallel, the second genetic sequence to the first genetic sequence, the plurality of permutations of the first genetic sequence, the third genetic sequence, and the plurality of permutations of the third genetic sequence; and providing a second result for the second plane based, at least in part, on the comparing. Angizi teaches that the main memory rank is a set of MRAM chips, each divided into multiple Banks, each bank consisting of multiple memory matrices (mats) ( i.e. , tile ), each mat consisting of multiple computation memory sub-arrays ( i.e. , a plane in a plurality of planes ) (p. 2-3, section 2 ALIGNS ARCHITECTURE; Figure 1). Angizi teaches that in order to enable fast memory access and parallel in-memory computing, the data in BWT, Marker Table, and Suffix Array have to be reconstructed and saved into different memory arrays, banks, and chips (p. 3, col. 1, par. 2; p. 4, col. 1, par. 3 through p. 5, col. 1, par. 1; Figure 7), which reads on the plane and the second plane being located on different tiles of the APM device. Angizi teaches that each sub-array is searched in parallel for matches between the current input nucleotide and the BWT index (p. 4, col. 2, par. 2 through p. 5, col. 1, par. 2; Figures 7-8) . Claim Rejections - 35 USC § 103 07-20-aia AIA The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action: A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made. 07-23-aia AIA The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows: 1. Determining the scope and contents of the prior art. 2. Ascertaining the differences between the prior art and the claims at issue. 3. Resolving the level of ordinary skill in the pertinent art. 4. Considering objective evidence present in the application indicating obviousness or nonobviousness. 07-20-02-aia AIA This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention. 07-21-aia AIA Claim s 3-4 are rejected under 35 U.S.C. 103 as being unpatentable over Angizi , as applied to claims 1-2 in the above 35 USC 102 rejection, in view of Kaplan et al. (IEEE Micro, 2017, 37(4):20-28; newly cited) . Regarding claims 3-4 , Angizi teaches claims 1-2 as described above. Claim 3 further adds padding at least one row of the plurality of rows of the subsequent plurality of columns with data corresponding to "don't cares.". Claim 4 further adds that a number of the rows of the plurality of rows padded with "don't cares" corresponds to a number of nucleotides by which the first genetic sequence is shifted. Angizi doesn’t teach the limitations of claims 3-4. However, the prior art to Kaplan discloses a processing-in-storage architecture based on Resistive CAM (ReCAM) for Smith-Waterman sequence alignment to find matching base pairs (abstract). Kaplan teaches that sequence A and sequence B are compared in a dynamic programming matrix, and sequence B is shifted one ReCAM row down in order for all to-be-matched base pairs to reside in the same ReCAM rows (p. 24, col. 2, par. 2 through p. 25, col. 1, par. 1). Kaplan teaches that the down-shifted columns require zero-padding of the top-most ReCAM row (p. 25, col. 1, par. 1; sections 1 and 2 of Figure 3). Regarding claims 3-4 , it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Angizi and Kaplan because both reference disclose methods and architecture for processing-in-memory sequence comparison. The motivation to include the padded cells as taught by Kaplan would have been to account for down-shifted columns during the sequence comparison of sequences A and B, as taught by Kaplan (p. 25, col. 1, par. 1; sections 1 and 2 of Figure 3). Therefore, it would have been obvious to pad the cells of the sequence as it was circularized while generating the BW matrix in Angizi. Double Patenting 08-33 AIA The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg , 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman , 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi , 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum , 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel , 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington , 418 F.2d 528, 163 USPQ 644 (CCPA 1969). A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA. A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b). The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13. The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA/25, or PTO/AIA/26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer. Claims 1-2 and 5-10 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4 and 7 of copending Application No. 18/049,498 in view of Angizi et al. (Proceedings of the 56th Annual Design Automation Conference, 2019 , p. 1-6; newly cited). Claims 3-4 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 3-4 of copending Application No. 18/049,498 in view of Angizi, as applied to claims 1-2, and further in view of Kaplan et al. (IEEE Micro, 2017, 37(4):20-28; newly cited). These are provisional nonstatutory double patenting rejection s because the patentably indistinct claims have not in fact been patented. Reference claim 1 discloses the limitations of instant claim 1 except for “comparing, in parallel”. However, the prior art to Angizi discloses a local data partitioning, mapping, and pipeline technique to maximize the parallelism in multiple computational sub-array while doing the alignment task (abstract). Reference claims 3-4 disclose the limitations of instant claim 2 . The reference application does not disclose the limitations of instant claims 3-4 . However, the prior art to Kaplan discloses a processing-in-storage architecture based on Resistive CAM (ReCAM) for Smith-Waterman sequence alignment to find matching base pairs (abstract). Kaplan teaches that sequence A and sequence B are compared in a dynamic programming matrix, and sequence B is shifted one ReCAM row down in order for all to-be-matched base pairs to reside in the same ReCAM rows (p. 24, col. 2, par. 2 through p. 25, col. 1, par. 1). Kaplan teaches that the down-shifted columns require zero-padding of the top-most ReCAM row (p. 25, col. 1, par. 1; sections 1 and 2 of Figure 3). The reference application does not disclose the limitations of instant claim 5 . However, Angizi teaches a read searching operation ( i.e. , a result for the plane ) to compare reads with the stored BW matrix of the reference sequence in the sub-array in a parallel manner, (p. 4, col. 1, par. 2 and col. 2, par. 3 through p. 5, col. 1, par. 1; Figures 5 and 7). As Angizi teaches comparing multiple reads, and gives an example of a current input nucleotide (p. 4, col. 2, par. 3), it is considered that Angizi fairly teaches comparing a third genetic sequence in parallel to the stored permutations of the first genetic sequence and providing a second result for the plane as instantly claimed. Reference claim 2 discloses the limitations of instant claim 6 . Reference claim 7 discloses the limitations of instant claim 7 . Reference claim 7 discloses the limitations of instant claim 8 . The reference application does not disclose the limitations of instant claim 9 . However, Angizi teaches that in order to enable fast memory access and parallel in-memory computing, the data in BWT, Marker Table, and Suffix Array have to be reconstructed and saved into different memory arrays, banks, and chips (p. 3, col. 1, par. 2; p. 4, col. 1, par. 3 through p. 5, col. 1, par. 1; Figure 7). It is considered that as Angizi teaches distributing the storage of the BWT, Marker Table, and Suffix Array across memory arrays, and as Angizi teaches that the BWT, Marker Table, and Suffix Array are generated from a BW matrix of a circulated and sorted string of nucleotide sequences (p. 3, col. 2, par. 1; Figure 4), it is considered that some of those distributed BWT, Marker Table, and Suffix Array would overlap by at least one nucleotide as instantly claimed. Reference claim 7 discloses the limitations of instant claim 10 . Regarding claims 1-2 and 5-10 , it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application and Angizi because both references disclose processing-in-memory (PIM) devices for read alignment to a reference genome. The motivation to use the device as taught by Angizi would have been to provide energy efficient and parallel processing-in-memory acceleration of DNA short read alignment, as taught by Angizi (abstract). Regarding claims 3-4 , it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the reference application in view of Angizi and Kaplan because each reference discloses methods and architecture for processing-in-memory sequence comparison. The motivation to include the padded cells as taught by Kaplan would have been to account for down-shifted columns during the sequence comparison of sequences A and B, as taught by Kaplan (p. 25, col. 1, par. 1; sections 1 and 2 of Figure 3). Therefore, it would have been obvious to pad the cells of the sequence as it was shifted in the reference application. Conclusion No claims are allowed. Inquiries Any inquiry concerning this communication or earlier communications from the examiner should be directed to JANNA NICOLE SCHULTZHAUS whose telephone number is (571)272-0812. The examiner can normally be reached on Monday - Friday 8-4. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached on (571)272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only. For more information about the PAIR system, see https://ppair-my.uspto.gov/pair/PrivatePair. Should you have questions on access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative or access to the automated information system, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685 Application/Control Number: 18/049,506 Page 2 Art Unit: 1685 Application/Control Number: 18/049,506 Page 3 Art Unit: 1685 Application/Control Number: 18/049,506 Page 4 Art Unit: 1685 Application/Control Number: 18/049,506 Page 5 Art Unit: 1685 Application/Control Number: 18/049,506 Page 6 Art Unit: 1685 Application/Control Number: 18/049,506 Page 7 Art Unit: 1685 Application/Control Number: 18/049,506 Page 8 Art Unit: 1685 Application/Control Number: 18/049,506 Page 9 Art Unit: 1685 Application/Control Number: 18/049,506 Page 10 Art Unit: 1685 Application/Control Number: 18/049,506 Page 11 Art Unit: 1685 Application/Control Number: 18/049,506 Page 12 Art Unit: 1685 Application/Control Number: 18/049,506 Page 13 Art Unit: 1685 Application/Control Number: 18/049,506 Page 14 Art Unit: 1685 Application/Control Number: 18/049,506 Page 15 Art Unit: 1685 Application/Control Number: 18/049,506 Page 16 Art Unit: 1685 Application/Control Number: 18/049,506 Page 17 Art Unit: 1685
Prosecution Insights