DETAILED ACTION
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 .
Status of the Claims
Claims 1-22 are under examination.
Claim Rejections - 35 USC § 103
2. In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
Claims 1-6, 8-14, 16, 18-19, and 21-22 are rejected under 35 U.S.C. 103 as being unpatentable over Muerdter et al. (WO 2022/040573 A2) in view of Gorla et al. (US 2022/0172120).
Regarding claims 1, 12, and 18, Muerdter et al. teach a method and system for identifying regulatory elements (abstract, paragraph [0050]); on a system with a non-transitory computer-readable medium with executable instructions that cause a processor to execute the method (paragraphs [0040], [00140]-[00142], [00146], figure 15); identifying an input sequence associated with a regulatory element as a start sequence (paragraphs [0004] and [0010]); calculating a score for the start sequence, based on a scoring function (paragraphs [0004] and [0010]).
However, Muerdter et al. do not disclose initializing N iterations, altering at least one nucleotide in an input for each iteration, calculating a score for the altered sequence, advancing the altered sequence to a next iteration, and identifying the altered sequence as the output sequence for the N iterations, where the iteration is equal to N, and then after the N iterations, direct the output sequence to a validation phase where the regulatory element is synthesized.
Regarding claims 1, 11, 12, and 18, Gorla et al. disclose initializing N iterations on ate least one parameter where N is an integer (abstract, claim 1); for each of N iterations, altering at least one nucleotide in receiving an input sequence for the iteration (abstract, figures 1-3, paragraphs [0035]-[0039]); calculating a score for the altered sequence based on the scoring function (Figure 3, paragraph [0039]); advancing the altered sequence to a next iteration based on at least the calculated score for the altered sequence and a threshold (paragraph [0065]); identifying the altered sequence as an output sequence for the N iterations when the calculated score for the altered sequence indicates an enhance over the input sequence and the iteration is equal to N (figure 3, paragraph [0045]); and then after N iterations, directing the output sequence to a validation phase, whereby the sequence defining the regulatory element is synthesized (Figure 3, paragraphs [0002], [0046], and [0047]).
Regarding claim 2, Gorla et al. teach advancing the altered sequence to the next iteration is based on the calculated score for the altered sequence being greater than the calculated score for the start sequence (paragraphs [0023] and [0026]).
Regarding claim 3, Gorla et al. teach where advance the altered sequence to the next iteration is based on the iteration being less than N (paragraph [0065]).
Regarding claim 4, Gorla et al. where advancing the altered sequence to the next iteration is based on a probability function (paragraph [0023]).
Regarding claim 5, Gorla et al. teach discarding the altered sequence in response to the calculated score for the altered sequence being less than the calculated score for the start sequence (paragraph [0023]; claim 10).
Regarding claims 6 and 14, Muerdter et al. disclose where the regulatory element is a promoter, intron, or untranslated region (paragraph [0004], [0005], and [0044]).
Regarding claim 8, Gorla et al. disclose wherein advancing the altered sequence to the next iteration, based on a probability function satisfying the threshold and the iteration being less than N and wherein the threshold includes one of the static threshold and a randomly generated threshold per iteration (paragraphs [0019], [0020], [0065], and claim 1]).
Regarding claims 9 and 16, Gorla et al. teach where the probability function is p=exp[(E’-E)/T] (paragraph [0023]).
Regarding claims 10 and 22, Muerdter et al. teach where the parameter is temperature (paragraph 00139]). Gorla et al. teach where N is less than 100 (paragraph 0045]).
Regarding claims 13 and 19, Gorla et al. teach advancing the altered sequence to the next iteration is based on the calculated score for the altered sequence being greater than the calculated score for the start sequence (paragraphs [0023] and [0026]) and the iteration being less than N (paragraph [0065]).
Regarding claim 21, Gorla et al. disclose wherein advancing the altered sequence to the next iteration, based on a probability function satisfying the threshold and the iteration being less than N and wherein the threshold includes one of the static threshold and a randomly generated threshold per iteration (paragraphs [0019], [0020], [0065], and claim 1]) where the probability function incudes p=exp[(E’-E)/T] (paragraph [0023]).
It would have been obvious to one of ordinary skill in the art, at the time of filing, to modify the teachings of Muerdter et al. with the teachings of Gorla et al. The teachings of Gorla et al. provide the benefit of identifying weights to be employed in the selection algorithm associated with plant advancement to produce desired offspring having desired characters or combinations of characteristics (Gorla et al., paragraphs [0002] and [0011]). One of ordinary skill in the art would have been motivated to modify the teachings of Muerdter et al. with Goral et al. to gain this benefit. Furthermore, one of ordinary skill in the art would have had an expectation of success because the data analysis of each reference is combinable.
Allowable Subject Matter
4. Claims 7, 15, 17, and 20 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JERRY LIN whose telephone number is (571)272-2561. The examiner can normally be reached T-F 7am-5pm.
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/JERRY LIN/Primary Examiner, Art Unit 1685
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