DETAILED ACTION
Applicant’s response, filed 20 Jan. 2026, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Claims 4, 10-11, and 17 are cancelled.
27-38 are newly added.
Claims 1-3, 5-9, 12-16, and 18-38 are pending.
Claims 1-3, 5-9, 12-16, and 18-38 are rejected.
Claims 36-38 are objected to.
Priority
The effective filing date for the instant application is 24 Feb. 2021.
Claim Objections
Claims 36-38 are objected to because of the following informalities. This objection is newly recited and necessitated by claim amendment.
Claims 36-38 recite “2828 nt”, which should use the full form of the word before the abbreviation, and should recite “2828 nucleotides” (or “2828 nucleotides (nt)”).
Appropriate correction is required.
Claim Interpretation
Claim 13 recites “…wherein a combined edge cost for each target sequence [unit] is obtained by: obtaining frequencies…in the given unit DFA; taking a relative ratio of the frequency of the given path…”. The “given unit DFA” is interpreted to refer to the DFA for which a given target sequence unit is a part of and the “given path” is interpreted to refer to the path corresponding to a respective target sequence, given claim 9 recites “each DFA has one or more paths….,each path represents a target sequence unit”.
Claim Rejections - 35 USC § 112(a)
The rejection of claims 21-26 under 35 U.S.C. 112(a) in the Office action mailed 23 Oct. 2025 has been withdrawn after further consideration. Applicant’s originally filed claim 3 provides support for the protein sequence comprising multiple amino acids (i.e. at least two amino acids with no upper limit), and Applicant’s specification at para. [0043] and [0095] provide support for performing the method using a protein sequence having 1273 amino acids or 239 amino acids. Accordingly, Applicant’s disclosure provides support for using a protein sequence having at least two amino acids, including at least 1273 or 239 amino acids.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claims 33-38 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, at the time the application was filed, had possession of the claimed invention. This rejection is newly recited and necessitated by claim amendment.
Claims 33-35 recite “a protein sequence comprising at least 239 amino acids and not more than 1273 amino acids”. Claims 36-38 recite “a protein sequence comprising at least 1273 amino acids and not more than a number of amino acids corresponding to 2828 nt”, interpreted to mean at least a number of amino acids corresponding to 2828 nucleotides (942 amino acids) and not more than 1273 amino acids (see claim interpretation under 35 U.S.C. 112(b) below).
MPEP 2173.05(i) states any negative limitation or exclusionary proviso must have basis in the original disclosure. Furthermore, with respect to changing numerical range limitations, the analysis must take into account which ranges one skilled in the art would consider inherently supported by the discussion in the original disclosure. In the decision in In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976), the ranges described in the original specification included a range of "25%- 60%" and specific examples of "36%" and "50%." A corresponding new claim limitation to "at least 35%" did not meet the description requirement because the phrase "at least" had no upper limit and caused the claim to read literally on embodiments outside the "25% to 60%" range, however a limitation to "between 35% and 60%" did meet the description requirement. See MPEP 2163.05 III.
In the instant case, Applicant’s remarks filed 20 Jan. 2026 at pg. 1, para. 4 states support for the language of claims 33-35 is found at para. [0096], para. [0042], and para. [0097] of the specification. Applicant’s remarks filed 20 Jan. 2026, at pg. 1, para. 5, states support for this language of claims 36-38 is found at pg. 9, para. 42, pg. 28, para. 97, and at pg. 26, para. 93 where the Applicant expressly states the sequences “with length from 78 to 2828 nt” were used”. Applicant’s specification at [0093] provides support for a protein sequence with at least 26 amino acids and no more than 942 amino acids. Applicant’s specification at [0042] and [0096]-[0097] discloses an example of an EGFP protein with 239 amino acids and a spike protein containing 1,273 amino acids having a large number of mRNA candidates. However, Applicant’s specification does not provide support for protein sequences with amino acids specifically in the range of (1) 239 to 1273 amino acids or (2) 943 amino acids to 1273 amino acids, thus specifically excluding protein sequences (1) under 239 amino acids and over 1273 amino acids and (2) under 943 amino acids and over 1273 amino acids, in claims 33-35 and claims 36-38 respectively.
For the reasons discussed above, the specification does not provide a sufficient disclosure of the limitations above recited in claims 33-38 to demonstrate to one of ordinary skill in the art that the inventor possessed the invention at the time the application was filed. THIS IS A NEW MATTER REJECTION. For more information regarding the written description requirement, see MPEP §2161.01- §2163.07(b).
Response to Arguments
Applicant's arguments filed 20 Jan. 2026 regarding 35 U.S.C. 112(a) have been fully considered but they are not persuasive with respect to the new grounds of rejection set forth above.
Applicant remarks that the written description rejection is inapposite because Applicant is not trying to claim a composition of matter with some percentage of a constituent, and there is no pending claim directed to a composition of matter (Applicant’s remarks at pg. 2, para. 3-5).
This argument is not persuasive. MPEP 2163.05 III. pertains to changing numerical range limitations, and is not limited to only claims of a composition of matter. MPEP 2163.05 explains the failure to meet the written description requirement of 35 U.S.C. 112(a) commonly arises when the claims are changed after filing to either broaden or narrow the breadth of the claim limitations, or to alter a numerical range limitation or to use claim language which is not synonymous with the terminology used in the original disclosure.
Applicant remarks the claims are a method that might be carried out with protein sequences of various lengths, and notes that the Examiner holds the view that unless the Examiner has set forth other numbers in the application as filed, then supposedly there is no written description for the carrying-out of the method for numbers other than 239 or 1273 (Applicant’s remarks at pg. 2, para. 4). Applicant then invites the reader to consider an example of a method for cutting lumber, and states similarly for the present claims, a method for carrying out particular steps of a protein sequence of any of various lengths, and further remarks that protein in nature exhibit a wide range of lengths, and the target of an mRNA vaccine typically contains hundreds or thousands of amino acids, and thus it is common knowledge that proteins in nature have a wide range of lengths and thus application was in possession of applying the methods of proteins to particular lengths (Applicant’s remarks at pg. 2, para. 6 to pg. 3, para. 1). Applicant further remarks the examples in the application are examples and not limits (Applicant’s remarks at pg. 3, para. 2-6).
This argument is not persuasive. It is understood that the claimed invention may be applied to proteins of any length, as encompassed by claim 3, for example, stating the protein sequence comprises multiple amino acids (i.e. of any length). However, MPEP 2163.05 states the failure to meet the written description requirement of 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph, commonly arises when the claims are changed after filing to either broaden or narrow the breadth of the claim limitations, or to alter a numerical range limitation or to use claim language which is not synonymous with the terminology used in the original disclosure. MPEP 2173.05(i) explains that any negative limitation or exclusionary proviso must have basis in the original disclosure (e.g. excluding particular protein sequences below or above a particular length of amino acids). Therefore, while it is common knowledge proteins can have a wide length of lengths, this does not provide support for narrowing the protein lengths to be a particular range and excluding proteins above or below particular lengths in the claims. For the reasons discussed in the above rejection, the disclosure does not provide support for the particular claimed ranges of protein lengths in claims 33-38
Regarding the examples in the application not being limits, MPEP 2163.05 II explains Applicant was not entitled to the benefit of a parent filing date when the claim was directed to a subgenus (a specified range of molecular weight ratios) where the parent application contained a generic disclosure and a specific example that fell within the recited range because the court held that subgenus range was not described in the parent application. In other words, simply because the specification provides a specific example, this does not provide support for a particular subgenus range containing the specific example.
Applicant remarks that para. [0093] of the specification states sequences “with length from 78 to 2828 nt” were used”, and thus application is in possession of applying the claimed invention to many different lengths, and not merely 239 or 1273 amino acids (Applicant’s remarks at pg. 3, para. 7-8).
This argument is not persuasive. It is agreed the specification provides support for limiting the length of the proteins to have sequences of a length of 78 to 2828 nucleotides. However, this does not provide support for the ranges recited in claims 33-38 for the reasons discussed in the above rejection.
Applicant remarks that para. 93 of the specification incorporates by reference the database Uniprot, which contains sequences of many lengths, including the Titin protein with a length of more than thirty-five thousand amino acids, and thus Applicant was in possession of the notion of applying the invention to sequences of many lengths, and further remarks since para. [0108] of the specification says the embodiments of the invention are for mRNA design, or other vaccine study or antibody development (Applicant’s remarks at pg. 3, para. 9 to pg. 4, para. 2).
This argument is not persuasive. As already discussed above, simply because the specification provides a specific example, this does not provide support for a subgenus range containing the specific example, and specifically excluding proteins less than or greater than the recited length. Furthermore, as discussed in the above rejection, para. [0093] states that 100 proteins from the Uniprot database with a length from 78 nucleotides to 2828 nucleotides were used (i.e. 26 to 942 amino acids).
Claim Rejections - 35 USC § 112(b)
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.
Claims 36-38 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention. This rejection is newly recited and necessitated by claim amendment.
Claims 36-38 are indefinite for recitation of “a protein sequence comprising at least 1273 amino acids and not more than a number of amino acids corresponding to 2828 nt”. Given there are 3 nucleotides per amino acid, 2828 nucleotides corresponds to 942 amino acids. Therefore it is unclear what range of amino acids the protein sequence is intended to be, given 942 amino acids is less than 1273 amino acids, but the claim requires the protein sequence has at least 1273 and not more than 942 amino acids. As a result, it is unclear if the protein sequence must be equal or greater to 1273 amino acids or if the protein sequence must be less than or equal to 942 amino acids. Clarification is requested. For purpose of examination, the claims are interpreted to mean that the protein has at least 942 amino acids and no more than 1273 amino acids.
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.
Claims 1-3, 5-9, 12-16, and 18-38 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. Any newly recited portion is necessitated by claim amendment.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 1, 9, and 16 being representative) is directed to a method and product for sequence design. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claims 1, 9, and 16 recite the following steps which fall under the mathematical concepts and/or mental processes groupings of abstract ideas:
building a unit deterministic finite automaton (DFA) for each of the multiple source sequence units, each unit DFA comprises multiple nodes including a start node and an end node, each DFA has one or more paths between the start node and the end node, each path comprises multiple edges with each edge coupled between two adjacent nodes (mental process and mathematical concept);
concatenating at least unit DFAs for the multiple source sequence units into a single DFA representing candidate target sequences that translate into the source sequence (mental process and mathematical concept);
intersecting a context free grammar (CFG) on the single DFA for an intersected CFG (mental process);
defining each nonterminal and start symbol in the intersected CFG (claim 1 only) (mental process);
defining one or more rules in the intersected CFG (claim 1 only) (mental process); and
searching in the intersected CFG for a desired target sequence having a sequence structure that minimizes an objective function, wherein the objective function comprises a minimum free energy (MFE) of a respective candidate targeted sequence and an additive regularization term, and the additive regularization term is an overall cost [of] traversing a full path of the respective candidate target sequence (mental process and mathematical concept).
The identified claim limitations falls into the group of abstract ideas of mental processes, for the following reasons. First, building a DFA with nodes and paths for each multiple source sequence unit (e.g. an amino acid), can be practically performed mentally aided via pen and paper by drawing a graph representing each amino acid with nodes ribonucleic acids representing the codon (see FIG. 1). Furthermore concatenating DFAs for multiple sources sequences can be practically performed in the mind by combining two DFAs via pen and paper to create a longer sequence. Next, intersecting a context free grammar on the single DFA amounts to a mere analysis of data, by applying a set of production rules to a DFG, as described in Applicant’s specification at para. [0057]-[0059]. Furthermore, defining each nonterminal and start symbol and rules in the intersected CFG amounts to a mental determination of variables of the CFG, which is a mental process. Last, searching in the intersected CFG for a desired target sequence having a sequence structure that minimized an objection function, including an MFE and additive regularization term of a cost of traversing a full path, encompasses performing addition and multiplication to determine a loss for each potential sequence and selecting a target sequence with the lowest cost, as described at para. [0077]-[0078] of the specification. See MPEP 2106.05(a)(2) III.
Furthermore, the limitations of building a unit deterministic finite automation for each of the multiple source sequence units, concatenating unit DFAs to a single DFA, and searching in the intersected CFG to minimize an objection function comprising an MFE and additive regularization term further recite a mathematical concept. Specifically, building DFAs and a single DFA made of concatenated DFAs recites a mathematical relationship, similar to the claims of organizing information and manipulating information through mathematical correlations in Digitech Image Techs., LLC v. Electronics for Imaging, Inc., 758 F.3d 1344, 1350, 111 USPQ2d 1717, 1721 (Fed. Cir. 2014). Furthermore, searching the intersected CFG by minimizing an objective function requires calculating losses/costs from the objective function to find an optimal target sequence, as described at para. [0077]-[0078] of the specification. Thus these limitations recite a mathematical concept. See MPEP 2106.04(a)(2) I.
Dependent claims 2-3, 5-8, 12-15, and 18-38 further recite an abstract idea and/or further limit the abstract idea of claims 1, 9, and 16. Dependent claim 2 further limits the CFG to be a stochastic CFG. Dependent claims 3 and 19 further limit the abstract idea of claims 1 and 16 to utilize a protein sequence comprising multiple amino acids. Dependent claims 5, 12, and 18 further limits the overall cost of claims 1, 9, and 16, and thus is part of the abstract idea. Dependent claim 6 further recites the mental process and mathematical concept of obtaining combined edge costs by obtaining frequencies of all codons, taking a relative ratio of the frequency of a codon to a highest frequency, and implementing a log operation. Dependent claims 7 and 15 further recite the mental process of initializing a singleton for a state, going through one or more pairing rules for state update for each state between two nodes, going through one or more bifurcation rules, keeping a predetermined number of states, and backtracing. Dependent claim 8 further recites back-tracing a plurality of top target sequences in a stored-order. Dependent claim 13 further limits how the combined edge costs were obtained, and thus are part of the abstract idea. Dependent claim 14 further recites the mental process and mathematical concept of adjusting a combined edge cost, adjusting combined edge costs of other paths using the adjustment amount, and applying the adjustment amount to one shared edge as an edge cost. Dependent claim 30 recites the mental process and mathematical concept of obtaining frequencies of codons, taking a relative ratio, and implementing a log operation for the CAI. Dependent claims 21-38 further limit the mental process and mathematical concept of building a DFA to be for a protein sequence. Therefore, claims 1-3, 5-9, 12-16, and 18-38 recite an abstract idea. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Claims 2-3, 5-6, 8, 12-14, and 18-20 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements of claims 1, 9, and 16 include:
a computer;
receiving a source sequence comprising multiple source sequence units (i. receiving data);
a non-transitory computer-readable medium; and
the searching/search carried out by means of a first and second hash tables stored in the computer/processor, the first hash table used to store a best score for each state therein, and the second hash table used to store a best backpointer for each state therein.
The additional element of dependent claims 7 and 15 include:
initializing a first hash table to store a best score for each state between two nodes in the single DFA and a second hash table to store a best backpointer for each state (i.e. storing data).
The additional element of dependent claims 21-38 include:
wherein the received source sequence is a protein sequence comprising at least 239 amino acids (claims 21-23);
wherein the recited source sequence is a protein sequence comprising at least 1273 amino acids (claims 24-26);
wherein the received source sequence is a protein sequence comprising 239 amino acids (claims 27-29);
wherein the received source sequence is a protein sequence comprising 1273 amino acids (30-32);
wherein the received source sequence is a protein sequence comprising at least 239 amino acids and not more than 1273 amino acids (claims 33-35); and
wherein the received source sequence is a protein sequence comprising at least 1273 amino acids and not more than a number of amino acids corresponding to 2828 nucleotides (claims 36-38).
The additional elements of a computer, non-transitory computer-readable medium, receiving data, and storing data are generic computer components and/or functions. Dependent claims 21-38 serve to further limit the data being received. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
Furthermore, while the claims utilize a hash table to store information that is used in the searching, the only discussion of the hash tables are at para. [0069] of the specification, and the specification does not provide any technical explanation that indicates an improvement to computer technology, or another technology. Instead, the claims merely invoke computers merely as a tool. Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016), and furthermore, merely link the abstract idea of searching the intersected CFG to a particular technological environment of hash tables, which is not an improvement to technology. See MPEP 2106.05(f) and 2106.05(h).
Therefore, the additionally recited elements merely invoke computers as a tool and/or generally link the use of the abstract idea to a particular technological environment, and as such, the claims as a whole do no integrate the abstract idea into practical application. Thus claims 1-3, 5-9, 12-16, and 18-38 are directed to an abstract idea. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception.
Claims 2-3, 5-6, 8, 12-14, and 18-20 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements of claims 1, 9, and 16 include:
a computer;
receiving a source sequence comprising multiple source sequence units (i. receiving data);
a non-transitory computer-readable medium; and
the searching/search carried out by means of a first and second hash tables stored in the computer/processor, the first hash table used to store a best score for each state therein, and the second hash table used to store a best backpointer for each state therein.
The additional element of dependent claims 7 and 15 include:
initializing a first hash table to store a best score for each state between two nodes in the single DFA and a second hash table to store a best backpointer for each state (i.e. storing data).
The additional element of dependent claims 21-38 include:
wherein the received source sequence is a protein sequence comprising at least 239 amino acids (claims 21-23);
wherein the recited source sequence is a protein sequence comprising at least 1273 amino acids (claims 24-26);
wherein the received source sequence is a protein sequence comprising 239 amino acids (claims 27-29);
wherein the received source sequence is a protein sequence comprising 1273 amino acids (30-32);
wherein the received source sequence is a protein sequence comprising at least 239 amino acids and not more than 1273 amino acids (claims 33-35); and
wherein the received source sequence is a protein sequence comprising at least 1273 amino acids and not more than a number of amino acids corresponding to 2828 nucleotides (claims 36-38).
The additional elements of a computer, non-transitory computer-readable medium, receiving data, and storing data are generic computer components and/or functions. Dependent claims 21-38 serve to further limit the data being received. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
Furthermore, the additional element of storing information in hash tables in the context of DFAs is well-understood, routine, and conventional. This position is supported by Garg et al. (A Review of DFA Minimizing State Machines Using Hash-Tables, 2013, IJCTT, 4(4), pg. 779-782; previously cited). Garg reviews deterministic finite automation (DFA) minimization using hash tables (Abstract), including that DFA minimization have applications in optimizing hashing techniques (pg. 779, col. 1, para. 3 to pg. 780, col. 1, para. 1). Garg further discloses it is well known that array searches are slower than Hash-Tables, and a Hash-Table is incredibly fast for the same purpose of implementing DFAs (pg. 782, col. 2, para. 2).
Last, as explained by the Supreme Court, a claim directed to a judicial exception cannot be made eligible "simply by having the applicant acquiesce to limiting the reach of the patent for the formula to a particular technological use." Diamond v. Diehr, 450 U.S. 175, 192 n.14, 209 USPQ 1, 10 n. 14 (1981). Thus, limitations that amount to merely indicating a field of use or technological environment in which to apply a judicial exception, such as storing data in a hash table, do not amount to significantly more than the exception itself, and cannot integrate a judicial exception into a practical application
Therefore, taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Response to Arguments
Applicant's arguments filed 20 Jan. 2026 regarding 35 U.S.C. 101 have been fully considered but they are not persuasive.
Applicant remarks that the Office action is dated October 23 2025, but is conspicuous by its absence is any indication that the important ex parte Desjardins decision was taken into account in the Office action, and that the patent Trial and Appeal Board has designated ex parte Desjardins to be precedential, and further remarks that the Examiner is requested to take into account the Director’s memo to the Patent Examining Corps dated December 4 2025 and the amendment to the MPEP entered on 5 Dec. 2025 (Applicant’s remarks at pg. 4, para. 3 to pg. 5, para. 1).
The above response has been fully considered, but does not appear to present any arguments. The rejections are maintained for the reasons set forth in the above rejection and in the previous Office action, even considering ex parte Desjardins, the Director’s memo, and amendment to the MPEP entered 5 Dec. 2025. Furthermore, it is noted that a mention of ex parte Desjardins is not required to make a prima facie case supporting a 35 U.S.C. 101 rejection, and Applicant has not explained how ex parte Desjardins pertains to the instant claims. See MPEP 2106.07(a) for formulating and supporting rejections for lack of subject matter eligibility.
Applicant further remarks the Examiner is invited to evaluate the claims as a whole and appreciate the improvement disclosed in the specification as discussed at pages 5-7 of the response filed 3 Jan. 2025 and reconsider the 101 rejections (Applicant’s remarks at pg. 5, para. 2-3).
This argument is not persuasive for the reasons discussed at para. [062]-[074] of the previous Office action mailed 23 Oct. 2025 regarding the alleged improvement to technology.
Double Patenting
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 1-3, 5-9, 12-16, and 18-38 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of copending Application No. 18/795,898 (reference application). Any newly recited portion is necessitated by claim amendment. Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding instant claims 1, 9, and 16, reference claims 1 and 19 disclose a computer-implemented method and computer program product for sequence design, comprising the following.
Reference claims 1 and 19 disclose obtaining a candidate target sequence that translates into a source sequence, based on the source sequence, which would require that a source sequence was received.. Reference claim 2 disclose the source sequence is a protein sequence with multiple amino acids. Reference claim 17 discloses the search is performed by means of the recited first and second hash tables.
Reference claim 11 discloses the limitations of building a unit deterministic finite automation (DFA) for each of the multiple source sequence units and concatenating at least unit DFAs for the multiple source sequence units into a single DFA, exactly as instantly claimed.
Reference claim 12 discloses the instant limitation of intersecting a context free grammar on the single DFA for an intersected CFG.
Reference claim 13 discloses the limitations of defining each nonterminal and start symbol in the intersected CFG and defining one or more rules in the intersected CFG.
Reference claim 1 discloses searching in the candidate target sequence for a desired target sequence having a sequence structure that minimizes an objective function, wherein the objective function comprises a minimum free energy (MFE) of the candidate target sequence and an additive regularization term. Furthermore, reference claims 12-13 disclose the searching is performed in the CFG as instantly claimed.
Further regarding instant claims 1, 9, and 16, the reference claims do not disclose the single DFA represents multiple target sequences. However, simply duplicating a number of candidate target sequences is not sufficient to distinguish over the reference claims; specifically, the court held that mere duplication of parts has no patentable significance unless a new and unexpected result is produced. In the instant case, simply using two target sequences instead of one does not change the structure of the claimed single DFA, and thus does not result in new and unexpected results.
Regarding instant claim 2, reference claim 10 discloses the CFG is a stochastic CFG.
Regarding instant claims 3 and 19, reference claim 2 discloses the limitation of instant claim 3.
Regarding instant claims 5, 12, and 18, reference claim 6 discloses the overall cost is of traversing each target sequence unit of the candidate target sequence (e.g. sum of combined edge costs for a respective candidate sequence, given a cost of traversing each target sequence unit is an edge cost). Reference claim 7 specifies the overall cost is a sum of costs for codons (i.e. target sequence units) on the candidate target sequence (i.e. each combined edge cost is associated to a codon on the respective candidate target sequence.
Regarding instant claims 6, 13, and 20, reference claims 8 and 15 disclose the limitations of reference claim 8.
Regarding instant claims 7 and 15, reference claim 17 discloses the limitations of instant claim 7.
Regarding instant claim 8, reference claim 18 discloses the limitations of instant claim 8.
Regarding instant claim 14, reference claim 16 discloses the limitations of instant claim 14.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding instant claims 21-38, reference claim 2 discloses the source sequence is a protein sequence comprising multiple amino acids (at least two amino acids), which encompasses the claimed amino acid ranges of 239 to 1273, 942 to 1273, 239, or 1273 amino acids. In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists. In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In re Woodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990).
Response to Arguments
Applicant's arguments filed 20 Jan. 2026 have been fully considered but they do not present any arguments regarding the provisional double patenting rejection.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685