DETAILED ACTION
Notice of 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 .
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 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.
Election/Restrictions
Applicant’s election without traverse of Group II in the reply filed on 05/07/2026 is acknowledged. In this instant application, claims 1-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention there being no allowable generic or linking claim. Claims 16-41 are being examined on the merits.
Status of the Claims
Claims 1-41 are pending.
Claims 1-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, as set forth in the Non-Final Office Action dated 11/3/2025.
Claims 16-41 are examined.
Claim 19, 21-22 and 32 are objected to.
Claims 16-41 are rejected.
Priority
This US Application 17/937,866 (10/04/2022) claims benefit of US Application 63/256,051 (10/15/2021), as reflected in the filing receipt mailed on 11/01/2022. The claims to the benefit of priority are acknowledged; and the effective filing date of claims 16-41 is 10/15/2021.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 11/11/2022, 09/25/2024 and 05/07/2026 were considered by the examiner.
Claim objections
Claims 19 and 21 are objected to because of the following informality: the recited "a type of organisms" should read "a type of organism."
Claim 22 is objected to because of the following informality: the recited "wherein the first set of one or more processors configured to receive" should read " wherein the first set of one or more processors is configured to receive" for proper grammar.
Claim 32 is objected to because of the following informality: the language of the claim appears to be incorrect. The recited "The system of, claim 30 wherein the first set of one or more processors are configured to: receive a false-positivity probability input; and of the probabilistic data structure; and set a false-positivity rate for the probabilistic data structure in accordance with the false- positivity probability input" presents improper punctuation and appears to include recited terms by mistake (i.e. as bolded in the preceding sentence). It is interpreted that claim 32 reads "The system of claim 30, wherein the first set of one or more processors are configured to: receive a false-positivity probability input; and set a false-positivity rate for the probabilistic data structure in accordance with the false- positivity probability input."
Appropriate correction is required.
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 16-41 are rejected under 35 U.S.C. 112(b)as being indefinite for failing to particularly point out and distinctly claim the subject matter the invention. Dependent claims are rejected similarly, unless otherwise noted below. The following issues cause the respective claims to be rejected under 112(b) as indefinite:
In claim 16, the relationship between "a first set of one or more nucleic acid sequences" (1st receive step) and "a first set of nucleic acid sequences" (1st create step) is unclear because it is not clear if said first sets refer to the same nucleic acid sequences or not. It is unclear if the same set of one or more nucleic acid sequences that is being received is also the one being stored in the first index. For compact prosecution, it is interpreted that said sets refer to the same set of nucleic acid sequences and that the “create” limitation should be amended to recite “create and store data in a first index representing the [[a]] first set of nucleic acid sequences”. Claim 23 should be amended similarly to avoid 112(b) issues caused by this amendment.
In claim 16, the relationship between " a second set of one or more nucleic acid sequences" (2nd receive step) and "a second set of nucleic acid sequences" (2nd create step) is unclear because it is not clear if said first sets refer to the same nucleic acid sequences or not. It is unclear if the same set of one or more nucleic acid sequences that is being received is also the one being stored in the second index. For compact prosecution, it is interpreted that said sets refer to the same set of nucleic acid sequences. Claim 23 should be amended similarly to avoid 112(b) issues caused by this amendment.
In claims 33 the recited "the plurality of reference nucleic acid sequences" requires but lacks clear antecedent. There is insufficient antecedent basis for this limitation in the claim as there is no previous recitation of a plurality of reference nucleic acid sequences. The rejection may be overcome by amending the limitation to clarify the described antecedent basis
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 16-41 are rejected under 35 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 §I). Abstract ideas include mathematical concepts and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)).
101 background
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Analysis of instant claims
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The instant claims are directed to a system (claims 16-38 and 41), a CRM (claim 39) and a method (claim 40); each of which falls within one of the categories of statutory subject matter..
[Step 1: claims 16-41: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Background
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Analysis of instant claims
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mathematical concepts (in particular mathematical relationships and formulas) and mental processes (in particular procedures for observing, analyzing and organizing information) as well as a law of nature or a natural phenomenon are as follows.
Mathematical concepts (in particular mathematical relationships and formulas) include:
• "querying the probabilistic data structure by data representing the sample nucleic acid sequence to responsively generate data indicating whether the sample nucleic acid sequence is a member of the set" (claim 31);
The claims identified above read on math. The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation and determined each element performed either in the mind and/or by mathematical operation. Without further detail as to the methodology involved in " querying the probabilistic data structure", under the BRI, one may simply, for example, use pen and paper to perform mathematical steps to arrive at the described steps. Further support for the mathematical techniques used in the claims is provided in the specification at [0107], which discloses that the probabilistic data structure may be organized into a logical tree pattern. Thus, the recited terms correspond to verbal equivalents of mathematical concepts because they constitute actions executed by a group of mathematical steps in a form of a mathematical algorithm; thus mathematical concepts (MPEP 2106.04(a)(2)). A mathematical concept need not be expressed in mathematical symbols, because "words used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). MPEP 2106.04(a)(2) pertains.
Mental processes, defined as concepts or steps practically performed in the human mind such as steps of observations, evaluations, judgments, analysis, opinions or organizing information include:
• "identify a target region to serve as a nucleic acid reference sequence that corresponds to one or more of the nucleic acid sequences in the first set and that discriminates against one or more of the nucleic acid sequences in the second set, wherein the identifying comprises: identifying, by the first index, the target region as a conserved region appearing in every nucleic acid sequence in the first set" (independent claims 16 and 39-41);
• "confirming, by the second index, that the conserved region appears in none of the nucleic acid sequences in the second set" (independent claims 16 and 39-41);
• "compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence" (independent claim 16);
• "create/creating and store/storing data in a first index representing a first set of nucleic acid sequences" (independent claims 16 and 39-41);
• "create/creating and store/storing data in a second index representing the second set of nucleic acid sequences" (independent claims 16 and 39-41);
• "identifying the target region comprises ensuring that the identified target region has a length that complies with the indicated target region base-length criteria" (claim 25);
• "set a false-positivity rate for the probabilistic data structure in accordance with the false- positivity probability input" (claim 32);
• "define an arrangement of the multi-level data structure in accordance with the multi- level data-structure arrangement input" (claim 35);
• "determining whether the index stores a data structure associated with a sub- string of the sample nucleic acid sequence" (claim 37); and
• "for each of the nucleic acid sequences in the first set, dividing the nucleic acid sequence into a plurality of sub-strings" (claim 38).
Under the BRI, the recited limitations are mental processes because a human mind is also sufficiently capable of identifying a nucleic acid target region based on data evaluation, discriminating sequences between indexes, confirming and comparing data, creating/storing indexes (i.e. making subsequences of a sequence), defining an arrangement of data, determining that an index stores data and dividing sequences into sub-strings using pen and paper.
Dependent claims 33-34 recite further steps that limit the judicial exceptions in independent claim 16 and, as such, also are directed to those abstract ideas. For example, claims 33-34 recite further details about the probabilistic data structured queried.
Furthermore, the instant claims recite a natural correlation by correlating a nucleic acid sequence naturally found in the body to the identification of a target sequence for an organism. (see MPEP 2106.04(b).I).
[Step 2A Prong One: claims 16-41: Yes ]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Background
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
Analysis of instant claims
Instant claims 16-18, 22-23, 25, 32, 35 and 38-41 recite additional elements that are not abstract ideas:
• "one or more processors" (independent claims 16 and 39-41);
• "memory" (independent claims 16 and 39-41);
• "receive/receiving genomic data representing a first set of one or more nucleic acid sequences" (independent claims 16 and 39-41);
• "receive/receiving genomic data representing a second set of one or more nucleic acid sequences" (independent claims 16 and 39-41);
• "a portable kit for nucleic acid sequencing and sample identification, the portable kit comprising a second set of one or more processors and memory; wherein the first set of one or more processors are configured to cause transmission of data representing the target region to the portable kit for storage on the memory" (independent claim 16);
• "receiving a first user input indicating the one or more nucleic acid sequences; and receiving the genomic data representing the first set comprises receiving a second user input indicating the one or more nucleic acid sequences" (claim 17);
• "receive a length input indicating a base length for the target region to be identified" (claim 22);
• "receive an input indicating an index base-length to be used in creation of the first index; and creating and storing data in a first index representing the first set of nucleic acid sequences comprises representing the first set of nucleic acid sequences using subsequences having a length equal to the indicated index base-length" (claim 23);
• "receive an input indicating a target region base-length criteria to be used in identification of the target region" (claim 25);
• "receive a false-positivity probability input; and of the probabilistic data structure" (claim 32);
• "receive a multi-level data-structure arrangement input" (claim 35);
• "for each of the plurality of sub-strings, storing a data structure in the first index, wherein: the data structure indicates an identity of the nucleic acid sequence, a permutation of bases forming the sub-string, and a position of the sub-string in the nucleic acid sequence" (claim 38);
• "transmit data representing the target region to a portable kit for storage on memory of the portable kit, wherein the portable kit is configured to compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence" (independent claims 39-41).
Dependent claims 18-21 recite further details about the user input. Dependent claim 24 recite further details about the input indicating the index base length. Dependent claims 26-30 recite further details about the input indicating target regions. Dependent claim 36 recites further details about the data representing the target region.
Considerations under Step 2A, Prong Two
The recited limitations in claims 16-41 are interpreted as requiring the use of a computer. Hence, the claims explicitly recite steps executed by computers and therefore can be described as computer functions or instructions to implement on a generic computer.
Further steps directed to additional non-abstract elements of a computing device/computer do not describe any specific computational steps by which the "computer parts" perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions.
The judicial exceptions in the claims are considered to perform the claimed abstract idea with a computer, which is not sufficient to integrate an abstract idea into a practical application (see MPEP 2106.05(f)); since steps that can be performed mentally and merely performing the mental process in a computer environment do not negate the fact that something that can be carried out in the human mind. See MPEP 2106.04(a)(2).III.C.
The recited "portable kit for nucleic acid sequencing and sample identification" reads on mere instructions to apply the judicial exception, because the kit constitutes a computer.
Claims directed to "receiving" and "transmitting" data/input read on receiving or transmitting data over a network -Symantec, 838 F.3d at 1321 - MPEP 2106.05(a) pertains; which constitutes just necessary data gathering and therefore correspond to insignificant extra-solution activity.
Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)).
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements. Additional elements are further discussed in Step 2B below.
Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
[Step 2A Prong Two: claims 16-41: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during examination that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
Claims 16-41 recite a computer or computer functions, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions; which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
Further, the courts have found that receiving and transmitting/outputting data are well-understood, routine, and conventional functions of a computer when claimed in a generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versa ta Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(Il)(i)).
When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a broad technological environment. See MPEP 2106.05(a) and 2106.05(h).
The instant claims constitute insignificant extra solution activity, and when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(g)). Hence, these elements, when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(d)).
[Step 2B: claims 16-41: No]
Conclusion: Instant claims are directed to non-statutory subject matter
For the reasons above, the claims in this instant application, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept not clearly anything significantly more.
Claim Rejections - 35 USC § 103
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.
A. Claims 16-17, 22-31 and 39-41 are rejected under 35 U.S.C. 103(a) as being unpatentable over Marinier ("Neptune: a bioinformatics tool for rapid discovery of genomic variation in bacterial populations." Nucleic acids research 45(18):e159-e159 (2017)) in view of Deshpande ("Offline next generation metagenomics sequence analysis using MinION detection software (MINDS)." Genes 10(8):578 (2019)), as cited on the attached Form PTO-892.
Claim 16 recites:
receive genomic data representing a first set of one or more nucleic acid sequences;
create and store data in a first index representing a first set of nucleic acid sequences;
receive genomic data representing a second set of one or more nucleic acid sequences;
create and store data in a second index representing the second set of nucleic acid sequences; and
identify a target region to serve as a nucleic acid reference sequence that corresponds to one or more of the nucleic acid sequences in the first set and that discriminates against one or more of the nucleic acid sequences in the second set,
wherein the identifying comprises: identifying, by the first index, the target region as a conserved region appearing in every nucleic acid sequence in the first set; and
confirming, by the second index, that the conserved region appears in none of the nucleic acid sequences in the second set
• Marinier teaches a system called Neptune for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches (pg. 1 Abstract); wherein a genomic signature is defined as a string of nucleotides sufficiently unique to a user-specified set of targets called the inclusion group (i.e. first index representing a first set of nucleic acid sequences) (pg. 2 col. 2 para. 3) that discriminates it from a set of user-defined background targets called the exclusion group (i.e. second index representing a second set of nucleic acid sequences) aiming to locate unique and conserved regions within the inclusion group, but absent or minimally present in the exclusion group (i.e. identify a target region to serve as a nucleic acid reference sequence that corresponds to one or more of the nucleic acid sequences in the first set and that discriminates against one or more of the nucleic acid sequences in the second set) (pg. 3 col. 1 para. 1); wherein the candidate signatures outputted are guaranteed to contain, by default, no exact matches with any exclusion k-mer (i.e. confirming, by the second index, that the conserved region appears in none of the nucleic acid sequences in the second set) (pg. 6 col. 1 para. 3).
a portable kit for nucleic acid sequencing and sample identification, the portable kit comprising a second set of one or more processors and memory;
wherein the first set of one or more processors are configured to cause transmission of data representing the target region to the portable kit for storage on the memory;
wherein the second set of one or more processors are configured to compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence set
• Marinier does not teach the recitation above. However, Deshpande teaches a portable device with detection software MINDS for field sequencing (pg. 2 para. 2) and immediate analysis of the data, enabling rapid identification of bacteria, virus and fungi in a sample (pg. 2 para. 4); wherein reads were searched against an indexed database of all RefSeq bacterial and archeal genome sequences (i.e. compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence) downloaded periodically from Centrifuge developer’s website and stored locally (i.e. transmission of data representing the target region to the portable kit for storage on the memory) (pg. 3 para. 4).
Claim 17 recites:
wherein: receiving the genomic data representing the first set comprises receiving a first user input indicating the one or more nucleic acid sequences; and receiving the genomic data representing the first set comprises receiving a second user input indicating the one or more nucleic acid sequences
• Marinier teaches a system called Neptune for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches (pg. 1 Abstract); wherein a genomic signature is defined as a string of nucleotides sufficiently unique to a user-specified set of targets called the inclusion group (i.e. first index representing a first set of nucleic acid sequences) (pg. 2 col. 2 para. 3) that discriminates it from a set of user-defined background targets called the exclusion group (i.e. second index representing a second set of nucleic acid sequences) (pg. 3 col. 1 para. 1).
Claim 22 recites:
wherein the first set of one or more processors configured to receive a length input indicating a base length for the target region to be identified
• Marinier teaches the overview of Neptune’s signature discovery process for a single target reference, where the first step involves generating k-mers from all inclusion and exclusion targets with said k-mers being aggregated and provided as input to signature extraction (pg. 4 Fig. 1).
Claim 23 recites:
wherein: the first set of one or more processors is configured to receive an input indicating an index base-length to be used in creation of the first index; and creating and storing data in a first index representing the first set of nucleic acid sequences comprises representing the first set of nucleic acid sequences using subsequences having a length equal to the indicated index base-length.
• Marinier teaches a system called Neptune for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy (i.e. subsequences having a length equal to the indicated index base-length), while accommodating k-mer mismatches (pg. 1 Abstract); wherein Neptune uses the distinct k-mers found in each inclusion (i.e. input indicating an index base-length to be used in creation of the first index first index representing the first set of nucleic acid sequences) and exclusion target to identify sequences that are conserved within the inclusion group and absent from the exclusion group (pg. 3 col. 1 para. 2).
Claim 24 recites:
wherein: the input indicating the index base-length comprises one or more of the following: a user input explicitly specifying a number of bases; data characterizing processing resources of the first set of one or more processors; and data characterizing storage resources available for storage of the first index
• Marinier teaches that the k-mer length is automatically calculated unless provided by the user (i.e. a user input explicitly specifying a number of bases) (pg. 3 col. 1 para. 5).
Claim 25 recites:
wherein: the first set of one or more processors is configured to receive an input indicating a target region base-length criteria to be used in identification of the target region; and identifying the target region comprises ensuring that the identified target region has a length that complies with the indicated target region base-length criteria
• Marinier teaches the overview of Neptune’s signature discovery process for a single target reference, where the first step involves generating k-mers from all inclusion and exclusion targets with said k-mers being aggregated and provided as input (i.e. an input indicating a target region base-length criteria to be used in identification of the target region) to signature extraction (pg. 4 Fig. 1); wherein an inclusion k-mer is considered sufficiently represented when it is observed in a number of targets exceeding a minimum threshold (i.e. ensuring that the identified target region has a length that complies with the indicated target region base-length criteria) (pg. 4 col. 1 para. 2).
Claim 26 recites:
wherein the input indicating the target region base-length criteria comprises one or more of the following: a user input explicitly specifying a number of bases; data characterizing processing resources of the first set of one or more processors; data characterizing storage resources available for storage of the first index; data characterizing processing resources of the second set of one or more processors; and data characterizing storage resources available on the memory for storage of the conserved-signature sequences on the portable kit
• Marinier teaches that the k-mer length is automatically calculated unless provided by the user (i.e. a user input explicitly specifying a number of bases) (pg. 3 col. 1 para. 5).
Claim 27 recites:
wherein the input indicating the target region base-length criteria comprises data characterizing a base length of sample nucleic acid sequences generated by a sequencing system of the portable kit
• Marinier does not teach the recitation above. However, Deshpande teaches a portable device with detection software MINDS for field sequencing (pg. 2 para. 2) and immediate analysis of the data, enabling rapid identification of bacteria, virus and fungi in a sample (pg. 2 para. 4); wherein fragmentation length can also be controlled based on the volume and lysis time of the sample (pg. 3 para. 1) followed by reads acquisition and base-calling by software within the device (i.e. data characterizing a base length of sample nucleic acid sequences generated by a sequencing system of the portable kit) (pg. 3 para. 3).
Claim 28 recites:
wherein the data representing the target region comprises sequence data and associated metadata, wherein the associated metadata indicates an organism associated with the target region
• Marinier does not teach the recitation above. However, Deshpande teaches a portable device with detection software MINDS for field sequencing (pg. 2 para. 2) and immediate analysis of the data, enabling rapid identification of bacteria, virus and fungi in a sample (pg. 2 para. 4); wherein graphical interface allows users to straightforwardly submit the FASTQ file, input experimental metadata and conditions for associated information for an organism targeted as depicted in Fig. 3 generating intuitive data analysis (i.e. associated metadata indicates an organism associated with the target region) (pg. 10 Fig. 3).
Claim 29 recites:
wherein the data representing the target region comprises sequence data and associated metadata, wherein the associated metadata indicates a type of organism associated with the target region
• Marinier does not teach the recitation above. However, Deshpande teaches a portable device with detection software MINDS for field sequencing (pg. 2 para. 2) and immediate analysis of the data, enabling rapid identification of bacteria, virus and fungi in a sample (pg. 2 para. 4); wherein graphical interface allows users to straightforwardly submit the FASTQ file, input experimental metadata and conditions for associated information (i.e. including type of organism – hence species name) for an organism targeted as depicted in Fig. 3 generating intuitive data analysis (i.e. associated metadata indicates an organism associated with the target region) (pg. 10 Fig. 3).
Claim 30 recites:
wherein the data representing the target region comprises a probabilistic data structure that represents the target region as a member of a set
• Marinier teaches that Neptune’s loci discovery process identifies sequences that are sufficiently common to a group of target sequences (i.e. target region as a member of a set) and sufficiently absent from nontargets using probabilistic models (pg. 1 Abstract); wherein in order to facilitate parallelizable k-mer aggregation, the k-mers for each target may be organized into several output files where the k-mers in each file are unique to one target sharing the same initial sequence index (i.e. probabilistic data structure) (pg. pg. 3 col. 1 para. 4).
Claim 31 recites:
wherein comparing the target region to a sample nucleic acid sequence comprises querying the probabilistic data structure by data representing the sample nucleic acid sequence to responsively generate data indicating whether the sample nucleic acid sequence is a member of the set
• Marinier teaches that Neptune’s loci discovery process identifies sequences that are sufficiently common to a group of target sequences and sufficiently absent from nontargets using probabilistic models (pg. 1 Abstract); wherein the k-mers for each target may be organized into several output files where the k-mers in each file are unique to one target sharing the same initial sequence index (i.e. querying the probabilistic data structure by data representing the sample nucleic acid sequence) (pg. pg. 3 col. 1 para. 4) while signature discovery is guided with probabilistic models that make decisions with a measure of statistical confidence (i.e. responsively generate data indicating whether the sample nucleic acid sequence is a member of the set) (pg. 2 col. 2 para. 1).
Claim 39 recites:
receive genomic data representing a first set of one or more nucleic acid sequences;
create and store data in a first index representing a first set of nucleic acid sequences;
receive genomic data representing a second set of one or more nucleic acid sequences;
create and store data in a second index representing the second set of nucleic acid sequences;
identify a target region to serve as a nucleic acid reference sequence that corresponds to one or more of the nucleic acid sequences in the first set and that discriminates against one or more of the nucleic acid sequences in the second set, wherein the identifying comprises:
identifying, by the first index, the target region as a conserved region appearing in every nucleic acid sequence in the first set; and
confirming, by the second index, that the conserved region appears in none of the nucleic acid sequences in the second set
• Marinier teaches a system called Neptune for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches (pg. 1 Abstract); wherein a genomic signature is defined as a string of nucleotides sufficiently unique to a user-specified set of targets called the inclusion group (i.e. first index representing a first set of nucleic acid sequences) (pg. 2 col. 2 para. 3) that discriminates it from a set of user-defined background targets called the exclusion group (i.e. second index representing a second set of nucleic acid sequences) aiming to locate unique and conserved regions within the inclusion group, but absent or minimally present in the exclusion group (i.e. identify a target region to serve as a nucleic acid reference sequence that corresponds to one or more of the nucleic acid sequences in the first set and that discriminates against one or more of the nucleic acid sequences in the second set) (pg. 3 col. 1 para. 1); wherein the candidate signatures outputted are guaranteed to contain, by default, no exact matches with any exclusion k-mer (i.e. confirming, by the second index, that the conserved region appears in none of the nucleic acid sequences in the second set) (pg. 6 col. 1 para. 3).
transmit data representing the target region to a portable kit for storage on memory of the portable kit, wherein the portable kit is configured to compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence.
• Marinier does not teach the recitation above. However, Deshpande teaches a portable device with detection software MINDS for field sequencing (pg. 2 para. 2) and immediate analysis of the data, enabling rapid identification of bacteria, virus and fungi in a sample (pg. 2 para. 4); wherein reads were searched against an indexed database of all RefSeq bacterial and archeal genome sequences (i.e. compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence) downloaded periodically from Centrifuge developer’s website and stored locally (i.e. transmit data representing the target region to a portable kit for storage on memory of the portable kit, wherein the portable kit is configured to compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence) (pg. 3 para. 4).
Claim 40 recites:
receive genomic data representing a first set of one or more nucleic acid sequences;
create and store data in a first index representing a first set of nucleic acid sequences;
receive genomic data representing a second set of one or more nucleic acid sequences;
create and store data in a second index representing the second set of nucleic acid sequences;
identify a target region to serve as a nucleic acid reference sequence that corresponds to one or more of the nucleic acid sequences in the first set and that discriminates against one or more of the nucleic acid sequences in the second set, wherein the identifying comprises:
identifying, by the first index, the target region as a conserved region appearing in every nucleic acid sequence in the first set; and
confirming, by the second index, that the conserved region appears in none of the nucleic acid sequences in the second set
• Marinier teaches a system called Neptune for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches (pg. 1 Abstract); wherein a genomic signature is defined as a string of nucleotides sufficiently unique to a user-specified set of targets called the inclusion group (i.e. first index representing a first set of nucleic acid sequences) (pg. 2 col. 2 para. 3) that discriminates it from a set of user-defined background targets called the exclusion group (i.e. second index representing a second set of nucleic acid sequences) aiming to locate unique and conserved regions within the inclusion group, but absent or minimally present in the exclusion group (i.e. identify a target region to serve as a nucleic acid reference sequence that corresponds to one or more of the nucleic acid sequences in the first set and that discriminates against one or more of the nucleic acid sequences in the second set) (pg. 3 col. 1 para. 1); wherein the candidate signatures outputted are guaranteed to contain, by default, no exact matches with any exclusion k-mer (i.e. confirming, by the second index, that the conserved region appears in none of the nucleic acid sequences in the second set) (pg. 6 col. 1 para. 3).
transmitting data representing the target region to a portable kit for storage on memory of the portable kit, wherein the portable kit is configured to compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence.
• Marinier does not teach the recitation above. However, Deshpande teaches a portable device with detection software MINDS for field sequencing (pg. 2 para. 2) and immediate analysis of the data, enabling rapid identification of bacteria, virus and fungi in a sample (pg. 2 para. 4); wherein reads were searched against an indexed database of all RefSeq bacterial and archeal genome sequences (i.e. compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence) downloaded periodically from Centrifuge developer’s website and stored locally (i.e. transmit data representing the target region to a portable kit for storage on memory of the portable kit, wherein the portable kit is configured to compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence) (pg. 3 para. 4).
Claim 41 recites:
receive genomic data representing a first set of one or more nucleic acid sequences;
create and store data in a first index representing a first set of nucleic acid sequences;
receive genomic data representing a second set of one or more nucleic acid sequences;
create and store data in a second index representing the second set of nucleic acid sequences;
identify a target region to serve as a nucleic acid reference sequence that corresponds to one or more of the nucleic acid sequences in the first set and that discriminates against one or more of the nucleic acid sequences in the second set, wherein the identifying comprises:
identifying, by the first index, the target region as a conserved region appearing in every nucleic acid sequence in the first set; and
confirming, by the second index, that the conserved region appears in none of the nucleic acid sequences in the second set
• Marinier teaches a system called Neptune for rapidly locating differentially abundant genomic content in bacterial populations using an exact k-mer matching strategy, while accommodating k-mer mismatches (pg. 1 Abstract); wherein a genomic signature is defined as a string of nucleotides sufficiently unique to a user-specified set of targets called the inclusion group (i.e. first index representing a first set of nucleic acid sequences) (pg. 2 col. 2 para. 3) that discriminates it from a set of user-defined background targets called the exclusion group (i.e. second index representing a second set of nucleic acid sequences) aiming to locate unique and conserved regions within the inclusion group, but absent or minimally present in the exclusion group (i.e. identify a target region to serve as a nucleic acid reference sequence that corresponds to one or more of the nucleic acid sequences in the first set and that discriminates against one or more of the nucleic acid sequences in the second set) (pg. 3 col. 1 para. 1); wherein the candidate signatures outputted are guaranteed to contain, by default, no exact matches with any exclusion k-mer (i.e. confirming, by the second index, that the conserved region appears in none of the nucleic acid sequences in the second set) (pg. 6 col. 1 para. 3).
transmit data representing the target region to a portable kit for storage on memory of the portable kit, wherein the portable kit is configured to compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence.
• Marinier does not teach the recitation above. However, Deshpande teaches a portable device with detection software MINDS for field sequencing (pg. 2 para. 2) and immediate analysis of the data, enabling rapid identification of bacteria, virus and fungi in a sample (pg. 2 para. 4); wherein reads were searched against an indexed database of all RefSeq bacterial and archeal genome sequences (i.e. compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence) downloaded periodically from Centrifuge developer’s website and stored locally (i.e. transmit data representing the target region to a portable kit for storage on memory of the portable kit, wherein the portable kit is configured to compare the target region to a sample nucleic acid sequence to determine whether the target region matches the sample nucleic acid sequence) (pg. 3 para. 4).
Rationale for combining (MPEP §2142-2143)
Regarding claims 16-17, 22-31 and 39-41, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Marinier in view of Deshpande because all references disclose methods for discovery of genomic variation. The motivation would have been to incorporate a cost-effective option as well as quick turn-around time when analyzing samples in the field (pg. 1 Abstract Deshpande).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the discovery of genomic variation method of Marinier to the methods by Deshpande because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for discovery of genomic variation.
B. Claims 18-21 are rejected under 35 U.S.C. 103(a) as being unpatentable over Marinier and Deshpande as applied to claims 16-17 above further in view of Phillippy ("Insignia: a DNA signature search web server for diagnostic assay development." Nucleic acids research 37.suppl_2:W229-W234 (2009)), as cited on the attached Form PTO-892.
Claim 18 recites:
wherein the first user input comprises selection of an organism from a menu.
Claim 19 recites:
wherein the first user input comprises selection of a type of organisms from a menu.
Claim 20 recites:
wherein the second user input comprises selection of an organism from a menu.
Claim 21 recites:
wherein the second user input comprises selection of a type of organisms from a menu.
• Neither Marinier or Deshpande teach the recitations above. However, Phillippy teaches a web application for the rapid identification of unique DNA signatures (pg. 229 Abstract) with available menus (pg. 232 Fig. 2); wherein users are asked to select a reference genome, a set of target genomes, a background genome and a signature word length (i.e. reading on first and second user input as in claims 18-21) (pg. 230 col. 2 para. 4); wherein a database of all current bacterial and viral genomic sequences (pg. 229 col. 1 para. 2) is used by the user to select reference and target genomes (i.e. selection of an organism from a menu as in claims 18 and 20) (pg. 230 col. 2 para. 4); wherein the database is organized alphabetically and by type of organism (i.e. selection of a type of organisms from a menu as in claims 19 and 21) (pg. 230 col. 1 para. 4).
Rationale for combining (MPEP §2142-2143)
Regarding claims 18-21, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Marinier and Deshpande in view of Phillippy because all references disclose methods for discovery of genomic variation. The motivation would have been to quickly identify signatures for any combination of target and background genomes (pg. 229 col. 2 para. 1 Phillippy).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the discovery of genomic variation method of Marinier and Deshpande to the methods by Phillippy because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for discovery of genomic variation.
C. Claim 32 is rejected under 35 U.S.C. 103(a) as being unpatentable over Marinier and Deshpande as applied to claims 16 and 30 above further in view of Parker ("Field-based species identification in eukaryotes using real-time nanopore sequencing." (2017)), as cited on the attached Form PTO-892.
Claim 32 recites:
wherein the first set of one or more processors are configured to: receive a false-positivity probability input; and of the probabilistic data structure; and set a false-positivity rate for the probabilistic data structure in accordance with the false- positivity probability input
• Neither Marinier or Deshpande teach the recitation above. However, Parker teaches assessing the performance of field-sequenced and lab-sequenced read data to explore the utility of these data for species identification (pg. 4 para. 3); wherein estimated false -positive rates and estimated true positive rates were calculated during sample identification using field sequenced data (i.e. receive a false-positivity probability input) (pg. 13 Fig. 2) and the performance of statistics for binary classification of 'correct' and incorrect" identification was assessed by investigating the true and false positive rates (by reference to the known sample species) across a range of threshold difference values (i.e. set a false-positivity rate for the probabilistic data structure in accordance with the false- positivity probability input) (pg. 5 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claim 32, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Marinier and Deshpande in view of Parker because all references disclose methods for discovery of genomic variation. The motivation would have been to incorporate rapid specimen identification and genome wide analyses (pg. 2 para. 1 Parker).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the discovery of genomic variation method of Marinier and Deshpande to the methods by Parker because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for discovery of genomic variation.
D. Claims 33-35 are rejected under 35 U.S.C. 103(a) as being unpatentable over Marinier and Deshpande as applied to claims 16 and 30 above further in view of Bader ("Comprehensive and relaxed search for oligonucleotide signatures in hierarchically clustered sequence datasets." Bioinformatics 27(11):1546-1554 (2011)), as cited on the attached Form PTO-892.
Claim 33 recites:
wherein: the probabilistic data structure is stored as part of a multi-level data structure comprising a plurality of hierarchically-interrelated probabilistic data structures; probabilistic data structures in a first level of the multi-level data structure represent respective sets of the plurality of reference nucleic acid sequences; and probabilistic data structures in a second level of the multi-level data structure represent respective subsets of the sets of the plurality of reference nucleic acid sequences.
• Neither Marinier or Deshpande teach the recitation above. However, Bader teaches an algorithm for computing comprehensive collections of sequence- and sequence group-specific oligonucleotide signatures from large sets of hierarchically clustered nucleic acid sequence data (pg. 1546 Abstract) to reduce the probability of a signature being erroneous with the increasing number of group sequences in which it occurs (i.e. probabilistic model) (pg. 1552 col. 1 para. 2); wherein the proposed model consists of three computational stages: the first stage is the extraction of signature candidates from sequence data resulting in a bipartite graph relating sequences to signature candidates; the second stage performs hierarchical sorting of the signature candidates, resulting in a Bipartite Graph Representation Tree and the last stage extracts valuable signatures from the Bipartite Graph Representation Tree for each node in a hierarchical cluster – a phylogenetic tree (i.e. a plurality of hierarchically-interrelated probabilistic data structures; probabilistic data structures in a first level of the multi-level data structure represent respective sets of the plurality of reference nucleic acid sequences; and probabilistic data structures in a second level of the multi-level data structure represent respective subsets of the sets of the plurality of reference nucleic acid sequences) (pg. 1547 col. 1 para. 4).
Claim 34 recites:
wherein: data structures in the first level of the multi-level data structure represent respective sets of the plurality of reference nucleic acid sequences that are associated with a respective type of organism; and data structures in the second level of the multi-level data structure represent respective sets of the plurality of reference nucleic acid sequences that are associated with a respective organism.
• Neither Marinier or Deshpande teach the recitation above. However, Bader teaches the input data for the second and third stage of the proposed algorithm where the phylogenetic tree is labeled with group phynodes (Latin numerals) and organisms (leaves: Arabic numerals) and the bipartite graph showing which organisms (Arabic numerals) are matched by which signature candidates (capital letters) (pg. 1547 Fig. 1).
Claim 35 recites:
wherein: the first set of one or more processors are configured to: receive a multi-level data-structure arrangement input; and define an arrangement of the multi-level data structure in accordance with the multi- level data-structure arrangement input
• Neither Marinier or Deshpande teach the recitation above. However, Bader teaches that the proposed model consists of three computational stages: the first stage is the extraction of signature candidates from sequence data resulting in a bipartite graph relating sequences to signature candidates; the second stage performs hierarchical sorting of the signature candidates, resulting in a Bipartite Graph Representation Tree and the last stage extracts valuable signatures from the Bipartite Graph Representation Tree for each node in a hierarchical cluster – a phylogenetic tree (i.e. receive a multi-level data-structure arrangement input; and define an arrangement of the multi-level data structure in accordance with the multi- level data-structure arrangement input) (pg. 1547 col. 1 para. 4).
Rationale for combining (MPEP §2142-2143)
Regarding claims 33-35, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Marinier and Deshpande in view of Bader because all references disclose methods for discovery of genomic variation. The motivation would have been to incorporate a comprehensive search for sequence- and group-specific oligonucleotide signatures (pg. 1546 col. 2 para. 3 Bader).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the discovery of genomic variation method of Marinier and Deshpande to the methods by Bader because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for discovery of genomic variation.
E. Claims 36-38 are rejected under 35 U.S.C. 103(a) as being unpatentable over Marinier and Deshpande as applied to claim 16 above further in view of Macke ("RNAMotif, an RNA secondary structure definition and search algorithm." Nucleic acids research 29(22):4724-4735 (2001)), as cited on the attached Form PTO-892.
Claim 36 recites:
wherein: the data representing the target region comprises an index representing the target; the index comprises a plurality of data structures representing respective sub-string of the target region; and
the respective data structures are stored in the index and indicate an identity of the target region,
a permutation of bases forming the sub-string of the target region, and a position of the sub-string in the target region.
• Neither Marinier or Deshpande teach the recitation above. However, Macke teaches a motif search algorithm (pg. 4724 col. 2 para. 3) that describes an RNA structural elements and search any nucleotide sequence database (pg. 4724 Abstract); wherein a score is associated to each candidate found (pg. 4726 col. 1 para. 3); wherein built-in functions are used to access an attribute of the string that matches a specified sub-motif where the actual sequences that match each sub-motif are available as a set of string variables (i.e. a plurality of data structures representing respective sub-string of the target region) that are indexed (i.e. respective data structures are stored in the index and indicate an identity of the target region) to provide access to any sub-string of the current match (i.e. a position of the sub-string in the target region) (pg. 1926 col. 1 para. 5); wherein in one version of the descriptor bases were permutated in a circular fashion where the 5' and 3' sides of the motif were flipped (i.e. a permutation of bases forming the sub-string of the target region) (pg. 4729 col. 2 para. 1)
Claim 37 recites:
wherein: comparing the target region to a sample nucleic acid sequence comprises determining whether the index stores a data structure associated with a sub- string of the sample nucleic acid sequence.
• Neither Marinier or Deshpande teach the recitation above. However, Macke teaches built-in functions are used to access an attribute of the string that matches a specified sub-motif where the actual sequences that match each sub-motif are available as a set of string variables indexed (i.e. index stores a data structure associated with a sub- string of the sample nucleic acid sequence) to provide access to any sub-string of the current match (pg. 1926 col. 1 para. 5).
Claim 38 recites:
wherein: creating and storing data in the first index comprises: for each of the nucleic acid sequences in the first set, dividing the nucleic acid sequence into a plurality of sub-strings; for each of the plurality of sub-strings, storing a data structure in the first index, wherein: the data structure indicates an identity of the nucleic acid sequence, a permutation of bases forming the sub-string, and a position of the sub-string in the nucleic acid sequence.
• Neither Marinier or Deshpande teach the recitation above. However, Macke teaches a motif search algorithm (pg. 4724 col. 2 para. 3) that describes an RNA structural elements and search any nucleotide sequence database (pg. 4724 Abstract); wherein a score is associated to each candidate found (pg. 4726 col. 1 para. 3); wherein built-in functions are used to access an attribute of the string that matches a specified sub-motif where the actual sequences that match each sub-motif are available as a set of string variables (i.e. dividing the nucleic acid sequence into a plurality of sub-strings) that are indexed (i.e. , storing a data structure in the first index) to provide access to any sub-string of the current match (i.e. the data structure indicates an identity of the nucleic acid sequence) (pg. 1926 col. 1 para. 5); wherein in one version of the descriptor bases were permutated in a circular fashion where the 5' and 3' sides of the motif were flipped (i.e. a permutation of bases forming the sub-string of the target region) (pg. 4729 col. 2 para. 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 36-38, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Marinier and Deshpande in view of Macke because all references disclose methods for searching genomic sequences. The motivation would have been to incorporate a robust yet flexible RNA sequence search algorithm (pg. 4724 col. 2 para. 3 Macke).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the searching genomic sequences method of Marinier and Deshpande to the methods by Macke because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for searching genomic sequences.
Conclusion
No claims are allowed.
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/F.F.L./Examiner, Art Unit 1685
/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685
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