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 .
Claim Status
Claims 1-20 are rejected.
Priority
The instant application was filed on 09 September 2022 as such the effective filing date is 09 September 2022.
Information Disclosure Statement
The IDS was considered by the examiner.
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.
Specific deficiencies and the required response to this Office Action are as follows:
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.
Drawings
The drawings are objected to because Figures 3 and 4 include enumerated nucleotide sequences without providing sequence identifiers (see above). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because of the following informalities:
Page 8, line 16 contains a spelling mistake. The word “sore” should be corrected to “sort.”
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
Claim 15 is rejected under 35 U.S.C. 112(b), second paragraph, as being indefinite for failing to particularly pint out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 15 recites “receiving a request to compare the sequence of molecular nucleotides to a second sequence of molecular nucleotide” and “determining that a first nucleotide in the sequence of molecular nucleotides has a synthetic modification that is not present in a second nucleotide at a corresponding position in the second sequence of molecular nucleotides.” It is unclear which sequence is being compared to the “second sequence.” This rejection can be overcome by clearly specifying that the “second sequence” is being compared to a specified first or initial sequence.
Claim 15 recites “representing in the user interface presentation the synthetic modification that is not present in the second nucleotide using a symbol that is visually distinguished from other symbols in the user interface presentation.” It is unclear how the absence of the synthetic modification in the “second nucleotide” is being represented. The rejection can be overcome by indicating which symbol will be modified and which nucleotide representation will have this modified symbol.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more.
Step 2A, Prong 1
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step
1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claim 1 recites receiving a sequence of molecular nucleotides and generating a user interface with a base character representing the base of each nucleotide and symbols adjacent to the base character that represent synthetic modifications to the molecular nucleotide.
Claim 2 recites vertically stacked symbols
Claim 3 recites symbols above the base character.
Claim 4 recites visually distinguishable vertically stacked symbols to represent different synthetic modifications.
Claim 5 recites symbols with different shapes to represent the respective synthetic modification.
Claim 6 recites that the synthetic modifications are to the sugar and phosphate and the respective symbols for each are different.
Claim 7 recites the synthetic modifications to the sugar and phosphate are indicated by different symbol fill patterns.
Claim 8 recites being able to transition the user interface after requesting to zoom in.
Claim 9 recites that the synthetically modified sugar of a molecular nucleotide is represented by an outline of the base character of the zoomed in display format.
Claim 10 recites the synthetically modified base of a molecular nucleotide is represented by a shaded background in the zoomed in display format.
Claim 11 recites the synthetically modifies phosphate of a molecular nucleotide is represented by a single symbol adjacent to the base character in the zoomed in display format.
Claim 12 recites obtaining user-specified visual customizations for the synthetic modifications and updating the user interface display format according to the user-specified visual customizations.
Claim 13 recites different display colors for user-specified visual customizations of different types of synthetic modifications of the molecular nucleotides.
Claim 14 recites receiving a user-specified mapping between a first and second format and automatically converting the second format to the user-specified mapping.
Claim 15 recites receiving a request to compare two sequences of molecular nucleotides, determining the first sequence has a synthetic modification in the first nucleotide that is not present in the nucleotide in the comparable position of the second sequence, and representing this synthetic modification with a visually distinct symbol.
Claim 16 recites the user interface presentation having user-customizable grouping information for subsequences of the sequences of molecular nucleotides.
Claim 17 recites a user interface presentation that includes elements for editing labels for the subsequences at the beginning and end of the subsequences.
Claim 18 recites a user interface control for selecting additional synthetic modifications, receiving a selection to present additional alternate synthetic modifications, and modifying the symbols adjacent to the molecular nucleotide base character to represent the additional or alternate synthetic modifications.
Claim 19 recites one or more computers and one or more storage devices that can perform the operations of receiving the sequence of molecular nucleotides and generating a user interface with a base character representing the base of each nucleotide and symbols adjacent to the base character that represent synthetic modifications to the molecular nucleotide.
Claim 20 recites one or more non-transitory computer storage media to perform the operations of receiving the sequence of molecular nucleotides and generating a user interface with a base character representing the base of each nucleotide and symbols adjacent to the base character that represent synthetic modifications to the molecular nucleotide.
The limitations for the described methods of receiving a sequence of molecular nucleotides and generating representations to indicate synthetic modifications to components of molecular nucleotides are evaluations or judgements that can be made through mental observations or mathematical calculations which fall under the “mental processes” and “mathematical concepts” groupings of abstract ideas.
While claims 19-20 recite performing some aspects of the methods using an apparatus with computer processor(s) and computer program code or using non-transitory computer-readable media, there are no additional limitations that indicate that the processor and code require anything other than carrying out the recited mental process or mathematical concept in a generic computer environment. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation on generic computer components, then it falls into the “mental processes” grouping of abstract ideas. As such, claims 1-20 recite abstract ideas (Step 2A, Prong 1: YES).
Step 2A, Prong 2
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further
analyzed to determine if the claims as a whole integrate the recited judicial exception into a
practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a
practical application because the claims do not recite an additional element that reflects an
improvement to technology or applies or uses the recited judicial exception in some other
meaningful way. Rather, the instant claims recite additional elements that amount to mere
instructions to implement the abstract idea or insignificant extra-solution activity. Specifically, the claims recite the following additional elements:
Claim 1 recites providing a user interface presentation to a user device for display to a user.
Claim 19 recites performing the abstract steps with one or more processors and providing the user interface presentation to a user device for display to a user.
Claim 20 recites performing the abstract steps with a non-transitory computer-readable medium processors and providing the user interface presentation to a user device for display to a user.
There are no limitations that indicate that the processors or non-transitory computer-readable media require anything other than a generic computing system. As such, these limitations equate to mere instructions to implement the abstract ideas on a generic computer that the courts have stated do not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. In addition, mere display of collected and analyzed information that could be performed by the human mind do not render an abstract idea eligible. See Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016)
The above recited additional elements do not provide a practical application of the recited judicial exception. As such, claims 1-20 are directed to an abstract idea (Step 2A, Prong 2: NO).
Step 2B
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic computing environment.
As discussed above, there are no additional limitations to indicate that the claimed processors or non-transitory computer readable media require anything other than generic computer components in order to carry out the recited abstract ideas in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. In addition, mere display of collected and analyzed information that could be performed by the human mind do not render an abstract idea eligible. See Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016)
The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a
patent-eligible application of the judicial exception. Therefore, the claims do not amount to
significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-20
are not patent eligible.
Claim Interpretation
For the purposes of applying prior art:
Claim 15 is interpreted as receiving a request to compare a first sequence of a molecular nucleotides to a second sequence of molecular nucleotides; determining that a first nucleotide in the first sequence of molecular nucleotides has a synthetic modification that is not present in a second nucleotide at a corresponding position in the second sequence of molecular nucleotides.
Claim 15 is interpreted as representing in the user interface presentation the synthetic modification that is not present in the second nucleotide using a symbol on the second nucleotide that is visually distinguished from other symbols in the user interface presentation.
Claim Rejections - 35 USC § 102
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 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 –
(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.
Claims 1-13 and 16-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Sciabola et al. (PLOS ONE, 22 January 2021, pages 1-11) (Hereafter referred to as Sciabola.)
Regarding claim 1, Sciabola teaches “[a]n automated oligonucleotide selection procedure is available to quickly select one potential set of sequences with an appropriate property profile...[and]…[t]he selection protocol can be customized by the user through changes of the selection cutoffs or the addition of alternate design parameters and algorithms.” (Page 2, lines 40-43) In addition, Sciabola teaches that PFRED is “a software application for the design, analysis, and visualization of antisense oligo nucleotides and siRNA…” and “[t]he software provides an intuitive user-interface for scientists…” (page 1, lines 2-4) Sciabola further teaches “within PFRED are three oligonucleotide representations, … an explicit component or monomer view of the oligonucleotide breaking it down into sugars, bases and linkers. A sequence view is shown … using a standard notation with RNA(capital) and DNA (lowercase) but emphasizing “chemical modifications” through the use of the pink dots… a fully phosphorothioated backbone which is denoted by the pink dots between the base letters… three locked nucleic acids (LNAs) at the 3’ and 5’ ends of the compound that are distinguished by the pink dots above the letters denoting these nucleosides… [and] [t]he block representation was created to emphasize patterns of chemical modifications to a structure. Base modifications are shown as pink dots below the blocks, sugars are colored depending on their structure (e.g. LNA-yellow, 2’OMe-purple, etc.) and backbones other than phosphodiesters are represented by pink connectors above the blocks.” (Page 4, lines 7-18) Sciabola also teaches a user interface presentation and display through images in Figures 3, 4, and 5. (Pages 6 and 7)
Regarding claims 2, 3, 5, 7, 9, 10, and 13, the court found that aesthetic design changes which have no mechanical function cannot be relied upon to patentably distinguish the claimed invention from the prior art. In re Seid, 161 F.2d 229, 73 USPQ 431 (CCPA 1947
Regarding claim 4, Sciabola teaches a “block representation was created to emphasize patterns of chemical modifications to a structure. Base modifications are shown as pink dots below the blocks, sugars are colored depending on their structure (e.g. LNA-yellow, 2’OMe-purple, etc.) and back bones other than phosphodiesters are represented by pink connectors above the blocks.” (page 4, lines 15-18)
Regarding claim 6, Sciabola teaches “sugars are colored depending on their structure (e.g. LNA-yellow, 2’OMe-purple, etc.) and back bones other than phosphodiesters are represented by pink connectors above the blocks.” (Page 4, lines 16-18)
Regarding claim 7, Sciabola teaches “[b]ase modifications are shown as pink dots below the blocks.” (Page 4, line 16)
Regarding claim 8, Sciabola teaches a zooming in ability as noted by the magnifying glass symbol in figures 3 and 5. (Pages 6 and 7, note tool symbols at top of examples of user interface display figures)
Regarding claim 9, Sciabola teaches “sugars are colored depending on their structure (e.g. LNA-yellow, 2’OMe-purple, etc.).” (Page 4, lines 16-17)
Regarding claim 10, Sciabola teaches “[b]ase modifications are shown as pink dots below the blocks.” (Page 4, line 16)
Regarding claim 11, Sciabola teaches “a fully phosphorothioated backbone which is denoted by the pink dots between the base letters” and “backbones other than phosphodiesters are represented by pink connectors above the blocks.” (Page 4, lines 11-12 and 17-18)
Regarding claim 12, Sciabola teaches that “antisense oligonucleotides and siRNAs can be represented with HELM notation and different sequence visualization options can be created for specific purposes. Included within PFRED are three oligonucleotide representations.” (Page 4, lines 5-7)
Regarding claim 13, Sciabola teaches a “main PFRED table provides most of the common spreadsheet functions such as alphanumeric sorting, column/row resizing, column coloring and conditional coloring. In addition, users can choose which properties are displayed in the table and customize the display order.” (Page 3, lines 36-38) Sciabola further teaches that the “system includes a basic set of design algorithms but is extensible such that experienced developers can add novel or proprietary descriptors.” (Page 8, lines 34-35)
Regarding claim 16, Sciabola teaches a “system includes a basic set of design algorithms but is extensible such that experienced developers can add novel or proprietary descriptors. Workflows are included which walk researchers through the process of identifying a target sequence and choosing the design criteria to be applied in selection of candidate molecules. A series of oligonucleotide visualization and plotting algorithms are included along with spreadsheet functions allowing data import/export, formulas, and conditional formatting.” (Page 8, lines 34-39)
Regarding claim 17, Sciabola teaches options that show “locked nucleic acids (LNAs) at the 3’ and 5’ ends of the compound that are distinguished by the pink dots above the letters denoting these nucleosides.” (Page 4, lines 12-14)
Regarding claim 18, Sciabola teaches that the “system includes a basic set of design algorithms but is extensible such that experienced developers can add novel or proprietary descriptors” and a “series of oligonucleotide visualization and plotting algorithms.” (Page 8, lines 34-35 and 37-38)
Regarding claim 19, the instant application claims using a system of one or more computers and one or more storage devices coupled to the one or more computers to perform the methods of claim 1. The court held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art. See MPEP 2144.04 III.
Regarding claim 20, the instant application claims using a non-transitory computer-readable medium to implement the methods of claim 1. The court held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art. See MPEP 2144.04 III.
Claim Rejections - 35 USC § 103
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) 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.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claim 14-15 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Sciabola (PLOS ONE, 22 January 2021, pages 1-11) in view of Martin et al. (School of Life Sciences, 26 April 2019, pages i-100) (Hereafter referred to as Martin.)
Regarding claim 14, Sciabola teaches “[e]ach enumerated oligonucleotide is then aligned to the other selected transcripts.” (Page 5, lines 4-5) Sciabola further teaches alignment and comparison of two molecular nucleotide sequences and that “the user has the option to choose the Design type (siRNA design or AntiSense design) as well as additional oligo annotations (Off-target and Efficacy predictions) before triggering the Enumerate & Annotate button.” (Page 7, Figure 5: images and description)
Sciabola does not teach “automatically converting the data into the second format according to user specified mapping.”
Martin teaches that a user “may either perform an alignment with default settings, use one of the available presets, or customise [sic] the parameters…” (Page 53, section 5.1, lines 2-4)
It would have been prima facie obvious before the effective filing date for one of ordinary skill in the art to have applied to the method of Martin to automatically annotate a nucleotide sequence of Sciabola with customized user preferences. Martin further teaches that Jalview’s “primary function is the editing and visualization of sequence alignments, and their interactive analysis” and “[m]ultiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring [sic] and layout.” (page 2, section 1.1.2, lines 1-2 and 8-9) Sciabola teaches design considerations of oligonucleotide sequences, including specifically the “chemical modification pattern of nucleotides” (Page 2, line 20) Therefore, one of ordinary skill in the art would have been motivated to combine the features of Jalview allowing for customizable sequence alignment preferences and PFRED notating nucleotide modifications. The invention is therefore prima facie obvious.
Regarding claim 15, Sciabola teaches the comparison of multiple sequences of molecular nucleotides as shown in Figure 5. (Page 7) Sciabola further teaches that the “system includes a basic set of design algorithms but is extensible such that experienced developers can add novel or proprietary descriptors.” (Page 8, lines 34-35) In addition, Sciabola teaches a “block representation was created to emphasize patterns of chemical modifications to a structure. Base modifications are shown as pink dots below the blocks, sugars are colored depending on their structure (e.g. LNA-yellow, 2’OMe-purple, etc.) and back bones other than phosphodiesters are represented by pink connectors above the blocks.” (page 4, lines 15-18)
Sciabola does not teach “representing in the user interface presentation the synthetic modification that is not present in the second nucleotide using a symbol that is visually distinguished from other symbols in the user interface presentation” in regards to comparing two sequences of nucleotides.
Martin teaches that an “alignment (or each group defined on the alignment) will be divided into groups based on the residue or nucleotide found at that position. These new groups are annotated with the characters in the selected region, and Jalview’s group based conservation analysis annotation and colour [sic] schemes can then be used to reveal any associated pattern of sequence variation across the whole alignment.” (Page 65, section 6.2.3, lines 9-13)
It would have been prima facie obvious before the effective filing date for one of ordinary skill in the art to have applied to the method of Martin to modify annotations of aligned nucleotide sequences of Sciabola with distinguishing notations to indicate modification differences. Martin further teaches that Jalview’s “primary function is the editing and visualization of sequence alignments, and their interactive analysis” and “[m]ultiple visualizations of an alignment may be worked on simultaneously, and the user interface provides a comprehensive set of controls for colouring [sic] and layout.” (page 2, section 1.1.2, lines 1-2 and 8-9) Sciabola teaches design considerations oligonucleotide sequences, including specifically “chemical modification pattern of nucleotides” (Page 2, line 20) Therefore, one of ordinary skill in the art would have been motivated to combine the features of Jalview showing comparative notation between aligned sequences and PFRED indicating specific nucleotide modifications. The invention is therefore prima facie obvious.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Benchling Release Notes Volume V (April-May 2021) teaches a user interface to create, register, and model RNA oligos. Benchling Releases Notes Volume VII (June 2021) teaches modeling DNA and RNA oligo entities with chemical modifications on nucleotides, bulk editing modified oligonucleotides, using a symbol above the base character to represent a modification of the nucleotide, and using a circle around a base symbol as an identifier. Benchling Release Notes Volume VIII (July-August 2021) teaches Modified oligos can be filtered by monomer and nucleotide sequence template alignments. Zhang et al (Journal of Chemical Information and Modeling, 2012) teaches the HELM method of notation to represent nucleotide structures. Milton et al (Journal of Chemical Information and Modeling, 2017) teaches using HELM to model biopolymers. Boccaletto et al (Nucleic Acids Research, 2022) teaches a database of RNA modifications. Pennic (HIT Consultant, 2021) teaches some features of the release of Benchling RNA tools.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SHARON LEVINE GRAFF whose telephone number is (571)317-0219. The examiner can normally be reached Mon - Fri 7:30 AM - 4 PM.
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/S.L.G./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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