Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
2. Applicant’s election without traverse of Group I, claims 1-5, in the reply filed on 06 May 2026 is acknowledged.
The election of SEQ ID NO: 496 is not relevant at this time as no SEQ IDs are present in the claims of elected Group I.
Claim Rejections - 35 USC § 112
3. 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 applicant regards as his invention.
4. Claim 5 is 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.
Claim 5 recites the limitation "…by using the to-be-predicted sequence determined to comprise the IRES…" in lines 3 and 4. It is noted that claim 1, upon which claim 5 depends, does not require that the to-be-predicted sequences comprise the IRES. Therefore the limitations of claim 5 are conditional limitations to claim 1 and only apply to embodiments wherein the to-be-predicted sequences were determined to comprise the IRES. Therefore, there is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 101
5. 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.
6. Claims 1-5 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Claim 1 recites the steps “selecting n sequences comprising an IRES…” (a mental process), “subjecting the sample sequences and to-be-predicted sequences to one-hot encoding…” (a mathematical algorithm), “calculating a Levenshtein distance…” (a mathematical algorithm), “calculating an average…” (a mathematical algorithm), and “determining, based on the average…” (a mental process). Claims 2 and 3 disclose further mental processes related to comparing the results of the method of claim 1 to prediction thresholds, and while claim 4 recites an “experimental verification” step there is no language in the claim to indicate or specify that this step is not also drawn to a judicial exception (i.e., experimental verification performed in silico would be a mathematical algorithm).
This judicial exception is not integrated into a practical application because there are no specific limitations in claims 1-4 that are not related to the judicial exceptions. Claim 5 does not integrate the judicial exception into a practical application because it only recites limitations related to embodiments related to “…to-be-predicted sequences determined to comprise this IRES…”, however step (5) of claim 1 (from which claim 5 depends) does not require that the to-be-predicted sequences comprise an IRES at all. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because there are no required steps in addition to the judicial exceptions. The only claim that is not solely drawn to a judicial exception is claim 5, which does recite an experimental verification step that is not drawn to a judicial exception, however as discussed fully above and incorporated here claim 5 does not have proper antecedent basis in claim 1, only providing a conditional limitation depending on the “determining” process in step (5) of claim 1.
Conclusion
7. The closest prior art in relation to the instant claims is found in Gritsenko et al (Sequence features of viral and human internal ribosome entry sites predictive of their activity, PLOS Computational Biology, 13(9): e1005734, published 18 September 2017), Wang et al (IRESpy: an XGBoost model for prediction of internal ribosome entry sites, BMC Bioinformatics, 20, 409, published 30 July 2019) and Berger et al (Levenshtein distance, sequence comparison and biological database search, IEEE Transactions on Information Theory, 67, 6 published 20 May 2021). Gritsenko and Wang teach existing models for IRES prediction based on sample sets comprised of experimental validated IRES structures (Gritsenko, Wang; abstracts). These references use structural data, kmer words (i.e., sequences of a particular length) and random forest models to predict IRES activity after having trained a model on known IRES sequences. Berger describes Levenshtein distance calculations and their use in similarity searches and alignments between nucleic acid sequences (abstract). Neither Wang nor Gritsenko directly compare known IRES sample sequences to a to-be-predicted sequence (rather, they train a model to predict IRES motifs from unknown sequences), nor do they use one-hot encoding to categorized the nucleic acid bases, nor do they use Levenshtein distance averages between sample IRESes and to-be-predicted sequences to determine the presence of IRES sequences. Berger teaches the use of Levenshtein distance to rapidly calculate sequence similarities, but specifically teaches that modern bioinformatics heuristics such as K-mer matching (as used by Gritsenko and Wang) have partially supplanted the direct use of Levenshtein distance alignments (pg. 3292 column 2 ¶ 2).
8. No claims are allowed.
9. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-T 0800 - 1630.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682
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