DETAILED ACTION
Applicant's response, filed 03/18/2026, 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 .
Priority
This application filed 08/19/2022 is a National Stage entry of PCT/IL2021/050186, with an International Filing Date of 02/17/2021, and claims priority from Provisional Application 62978840, filed 02/20/2020. The claims are therefore examined as filed on 02/20/2020, the effective filing date. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further review of the priority application(s).
Claim Status
Claims 1-2 and 4-16 are pending.
Claim 3 is cancelled.
Claims 1-2 and 4-16 are examined.
Claims 1-2 and 4-16 are rejected.
Withdrawn Rejections
The rejection of claims 1, 3-14, and 16 under 35 U.S.C. §103 over SEMENYUK and KUBOKOVICH, in the Office action mailed 03/18/2026 is withdrawn in view of the amendments filed 06/17/2026, and persuasive argument that the cited references do not teach the amended limitations of identifying, as potential camouflage sections, unaligned sections of the query sequence positioned between a selected set of disjoint query substrings in the query sequence, removing a number of largest potential camouflage sections, and re-aligning the clean query sequence with the target sequence to generate a clean alignment score (remarks pg 11).
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 1-2 and 4-16 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of mental processes and mathematical concepts, without significantly more.
The MPEP at MPEP 2106 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of matter?
(2A)(1) Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea?
(2A)(2) Do the claims recite additional elements that integrate the judicial exception into a practical application?
(2B) If the claims recite a judicial exception and do not integrate the judicial exception, do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?
With regard to step (1) (Are the claims directed to a process, machine, manufacture or composition of matter?): Yes. The claims are directed to one of the statutory classes. Claims 1-2 and 4-16 are directed to a process (computer-based method).
With regard to step (2A)(1) (Do the claims recite a judicially recognized exception?): Yes. Claims 1-16 recite the abstract ideas of processing data using mental steps and mathematical concepts. Claims that recite nothing more than abstract ideas, natural phenomena, or laws of nature are not eligible for patent protection (see MPEP 2106.04).
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (See MPEP 2106.04(a)(2)). In particular, these abstract ideas include but are not limited to:
Applying an alignment algorithm to generate local alignments by aligning a substring of a sequence to a substring of the target sequence to maximize an alignment score (mental process/mathematical concept; the human mind is capable of aligning sequence strings to find the best/most matching, determining a score based on alignment is equivalent to performing a calculation; claim 1)
Selecting a set of disjoint query substrings from the aligned query substrings of the multiple local alignments (mental process; the human mind is capable of selecting a set of disjoint substrings from aligned substrings; claim 1)
Identifying, as potential camouflage sections, unaligned sections of the query sequence positioned between the disjoint query substrings in the query sequence (mental process; the human mind is capable of identifying a sequence based on alignment and positioning; claim 1)
Removing a number of potential camouflage sections from the query sequence to generate a clean sequence (mental process; the human mind is capable of removing sequence sections in an alignment to generate a new sequence; claim 1)
Applying a second alignment algorithm aligning the clean query sequence with the target to generate a clean alignment score (mental process/mathematical concept; the human mind is capable of applying an algorithm based on alignment, and computing a score based on the alignment is equivalent to performing a calculation; claim 1)
Reducing the clean alignment score by a gap removal penalty proportional to the number of largest potential camouflage sections removed (mental process/mathematical concept; the human mind is capable of applying a gap penalty in an alignment algorithm, and doing so to reduce/recalculate a score is equivalent to performing a calculation; claim 6)
Further adjusting the alignment score by addition of a probability of successful removal of the potential camouflage section (mental process/mathematical concept; the human mind is capable of adjusting a score using a probability, and doing so is equivalent to performing a calculation; claim 7)
Removing different numbers of alignment gaps to generate clean query sequences and reapplying the second alignment algorithm to generate clean alignment scores (mental process/mathematical concept; the human mind is capable of removing gaps and calculating a new score with an algorithm, doing so is equivalent to performing a calculation; claim 11)
Iterating generation of clean alignments and scores (mental process/mathematical concept; the human mind is capable of repeating alignment/calculation of scores, doing so is equivalent to performing a calculation; claim 12)
Dependent claims 2, 4-5, 8-10, 14-16 further limit the abstract ideas recited in the independent claims, and do not change their characterization as abstract ideas.
Therefore, the claims recite elements that constitute one or more judicial exceptions.
With regard to step (2A)(2) (Do the claims recite additional elements that integrate the judicial exception into a practical application?): No. Claim 1 and its dependents recite the additional elements of the method being “computer-based”, receiving a query sequence for screening against a target database, and outputting an alignment score indicating homology, with claim 11 providing further detail on the output score.
While the claims recite the additional element of receiving and outputting data, such steps that only amount to necessary data gathering and outputting, without any technical details of how the data is obtained/output that integrate the judicial exception, are insignificant extrasolution activities that do not add a meaningful limitation to the claims (see MPEP 2106.05(g)). As a result, the judicial exception is not integrated into a practical application. In addition, while the claims recite additional elements related to the use of computers, they do not provide any specific details by which the computer performs or carries out the judicial exception listed in step (2A)(1), nor do they provide any details of how specific structures of the computer are used to implement these functions. The judicial exception is therefore not integrated into a practical application because the generically recited computer elements do not add a meaningful limitation to the abstract idea, as they amount to simply implementing the abstract idea on a computer (see MPEP 2106.05(f)). Because the claims do not recite any additional elements that integrate the judicial exception into a practical application, the claims as a whole are directed to an abstract idea.
With regard to step (2B) (Do the claims recite additional elements that provide an inventive concept and amount to significantly more than the judicial exception?): No. The claims recite an abstract idea with additional elements; however, these additional elements are general computer elements added to abstract ideas, and non-particular instructions to apply the abstract idea by linking it to a field of use or extrasolution activity (see MPEP 2106.05(f-h)). General computer elements used to perform an abstract idea do not provide an inventive concept, and similarly, non-particular instructions to gather or produce data do not provide an inventive concept. Non-particular instructions to gather or output data are also considered well-understood, routine and conventional activities (see MPEP 2106.05(d), which indicates that limitations such as “Receiving or transmitting data over a network” from Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362, and “Storing and retrieving information in memory” from Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, are recognized as conventional activities). The claims therefore do not include additional elements that are sufficient to amount to significantly more than the judicial exception. As a result, the claims as a whole do not provide an inventive concept.
Response to Arguments – Rejections Under 35 USC § 101
Applicant’s arguments are unpersuasive. In the reply filed 06/17/2026, Applicant asserts that the characterization of the claims as a mental process or mathematical concept does not account for the ordered combination of claim steps (remarks pg 8). However, the ordered combination in which the abstract ideas are performed does not change their characterization as abstract ideas. Steps of aligning, selecting, identifying and removing substrings, and determining scores, are all abstract ideas.
The Applicant also asserts that any abstract ideas are integrated into a practical application, by addressing a specific problem in DNA sequence screening (pg 8-9). While the claims may recite a practical use in the general sense, they do not integrate the abstract idea into a “practical application” as defined by the MPEP 2106.04(d). In the MPEP, a “practical application” must be found among the non-abstract additional elements. Currently, the only additional elements in the claims are generic computer elements that allow the abstract idea to be implemented in a computer environment, and instructions to receive and output data, which are considered insignificant extrasolution activities, as indicated in the rejection above.
The Applicant further asserts that the claims are not eligible when considered as a whole (remarks pg 9). However, the claims as a whole are considered specifically because the claims are analyzed according to the analysis under steps 1, 2A1, 2A2 and 2B above. In order to be eligible as a whole, the claims must meet the criteria set out in these steps – they must be a statutory category, and if they recite abstract ideas, must recite an additional element that amounts to more than the judicial exception when combined with the abstract ideas. If the claim is directed to an abstract idea but contains no additional element that amounts to more than the judicial exception, it by definition cannot be eligible as a whole.
The Applicant also asserts that the claims do not merely apply an abstract idea on a general computer or limit an abstract idea to a field of use (remarks pg 9). However, there is nothing in the claims to indicate this – the claims are currently only directed to a computer based method of performing the abstract ideas, as the only additional elements are generic computer elements that allow the abstract idea to be implemented in a computer environment, and instructions to receive and output data.
As such, the claims remain rejected under 35 USC § 101.
Conclusion
No claims are allowed.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY C LEVERETT whose telephone number is (571)272-5494. The examiner can normally be reached 8:00am - 5:00pm M-Th.
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/M.C.L./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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