(12) INTERNATIONAL APPLICATION PUBLISHED UNDER THE PATENT COOPERATION TREATY (PCT)
`(19) World Intellectual Property
`Organization
`International Bureau
`
`(43) International Publication Date
`7 March 2013 (07.03.2013)
`
`WIPO!IPCT
`
`\=
`
`(10) International Publication Number
`WO 2013/030827 Al
`
`GD)
`
`International Patent Classification:
`G06F 19/22 (2011.01)
`G06F 19/26 (2011.01)
`
`(74)
`
`Agent: Dr. Eyal Bressler Ltd.; 11 Tuval St., Lazrom
`House, 52522 Ramat-Gan(IL).
`
`(21)
`
`International Application Number:
`
`PCT/IL2012/000326
`
`(81)
`
`(22)
`
`International Filing Date:
`
`(25)
`
`Filing Language:
`
`30 August 2012 (30.08.2012)
`
`English
`
`English
`
`Designated States (unless otherwise indicated, for every
`kind of national protection available): AE, AG, AL, AM,
`AO, AT, AU, AZ, BA, BB, BG, BH, BN, BR, BW, BY,
`BZ, CA, CH, CL, CN, CO, CR, CU, CZ, DE, DK, DM,
`DO, DZ, EC, EE, EG, ES, FI, GB, GD, GE, GH, GM, GT,
`HN, HR, HU,ID,IL, IN, IS, JP, KE, KG, KM, KN, KP,
`KR, KZ, LA, LC, LK, LR, LS, LT, LU, LY, MA, MD,
`ME, MG, MK, MN, MW, MX, MY, MZ, NA, NG, NI,
`Publication Language:
`NO,NZ, OM,PE, PG, PH, PL, PT, QA, RO, RS, RU, RW,
`Priority Data:
`(30)
`61/530,384—1 September 2011 (01.09.2011) US SC, SD, SE, SG, SK, SL, SM, ST, SV, SY, TH, TJ, TM,
`
`
`61/565,435
`30 November2011 (30.11.2011)
`US
`TN, TR, TT, TZ, UA, UG, US, UZ, VC, VN, ZA, 2M,
`61/594,323
`2 February 2012 (02.02.2012)
`US
`ZW.
`61/594,320
`2 February 2012 (02.02.2012)
`US (84) Designated States (unless otherwise indicated, for every
`Applicant (for ali designated States except US): GEN-
`kind of regional protection available): ARIPO (BW, GH,
`1818
`GM, KE, LR, LS, MW, MZ, NA, RW, SD, SL, SZ, TZ,
`OME COMPILER CORPORATION [US/US];
`UG, ZM, ZW), Eurasian (AM, AZ, BY, KG, KZ, RU, TJ,
`Allston Way, Berkeley, CA 94703 (US).
`T4), European (AL, AT, BE, BG, CH, CY, CZ, DE, DK,
`EE, ES, FI, FR, GB, GR, HR, HU,IE, IS, IT, LT, LU, LV,
`MC, MK, MT, NL, NO, PL, PT, RO, RS, SE, SI, SK, SM,
`TR), OAPI (BF, BJ, CF, CG, CI, CM, GA, GN, GQ, GW,
`ML, MR, NE, SN, TD, TG).
`
`(26)
`
`(71)
`
`(72)
`(75)
`
`
`
`
`
`wo2013/030827A1|IMINIITINAITAINNINISNAANATACAAA
`
`Inventors; and
`Inventors/Applicants (for US only): AMIRAV-DRORI,
`Omri [IL/L]; 5 Hayyar ally, 45269 Hod-Hasharon (IL).
`BEN MOSHE, Nir [IL/IL]; 43 Basel Street, 62744 Tel
`Aviv (IL).
`
`(54) Title: SYSTEM FOR POLYNUCLEOTIDE CONSTRUCT DESIGN, VISUALIZATION AND TRANSACTIONS TO MAN-
`UFACTURE THE SAME
`
`[Continued on next page]
`
`100
`
`(57) Abstract: The present invention disclose a computerized system for
`designing nucleic acid sequences for gene expression comprising; (a) a server
`[103] for hosting a database [106] (b) a network connection [102] and (c) a
`computer readable medium [101] comprising functional modules including
`(i) a design module for enabling designing of nucleic acid constructs; (ii) in-
`teractive user interface module for visualizing biological information relating
`to design operations; (iii) transaction module for purchasing a user-designed
`or pre-stocked nucleic acid constructs (iv) a detecting module for detecting
`designed nucleic acid sequences comprises harmful sequences; the systemis
`operating in a methodof: (a) visualizing biological information; (b) designing
`nucleic acid sequences; (c) detecting and notifying when harmful sequences
`are designed; (d) providing means for transactions regarding ordering and
`purchasing said synthesized nucleic acids.
`
` |
`
`
`GCCServer
`
`notification
`module
`
`
`
`Wf
`105
`
`Ww103
`
`
`
`
`
`
`a”
`|External
`
`
`data
`base
`
`
`
`106
`
`

`

`WO 2013/030827 A1IfMIMUTINIT INTEN TAG TTT TA ATAAU AAA
`
`Declarations under Rule 4.17: —_before the expiration of the time limit for amending the
`
`— as to applicant's entitlement to apply for and be granted
`claims and to be republished in the event of receipt of
`a patent (Rule 4.17(ii))
`amendments (Rule 48.2(h))
`Published:
`
`—_with international search report (Art. 21(3))
`
`

`

`WO 2013/030827
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`PCT/IL2012/000326
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`SYSTEM FOR POLYNUCLEOTIDE CONSTRUCT DESIGN, VISUALIZATION AND
`
`TRANSACTIONS TO MANUFACTURE THE SAME
`
`FIELD OF THE INVENTION
`
`‘The present
`
`invention relates in gencrally to a system for polynucleotide construct design
`
`visualization and transaction to manufacture the same
`
`BACKGROUND OF THE INVENTION
`
`The use of synthetic nucleic acid constructs for critical applications has never been greater.
`
`Synthetic nucleic acids are used in a variety of fields from life sciences research to applications
`
`involvingalternative sources of energy and beyond.
`
`For example, almost everything that our civilization needs or creates starts with finite resources
`
`of energy, such as oil, coal and natural gas with growing demand and dwindling supply. The
`
`prices of a great majority of commodities are going up. The need for renewable sources of
`
`biomass as an energy source is expanding. The use of synthetic nucleic acids to design living
`
`organisms for resources such as energy and food will be widespread into the future.
`
`To emphasize the magnitude of the problem and the opportunity,
`
`the department of energy
`
`released a 2004 report showing 120 high-value chemicals that can be bio-manufactured, each with
`
`a more than one billion dollar market size. The synthetic nucleic acid market for the source code
`
`of life is more than five hundred million dollars today.
`
`With the National Institutes of Health spending more than 1.5 billion dollars on manipulating
`
`DNA in 2008, this market is projected to grow to 3 billion dollars in 2015, with the market for
`
`synthetic biological products estimated at 4.5 billion dollars that same year.
`
`The creation of useful living organisms strongly relies on synthetic nucleic acids. The design and
`
`manipulation of nucleic acids traditionally has comprised the use of molecular biology, which is
`
`knownto be slow and error prone. The design of nucleic acids in a way that resembles typing ina
`
`1
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`WO 2013/030827
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`PCT/IL2012/000326
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`word processor would increase the ease and speed of editing, generating and synthesizing nucleic
`
`acid sequences as large as a genome.
`
`There is a need for treating the design and synthesis of nucleic acid sequences,
`
`leveraging the
`
`tools of information technology. Also, there is a need for efficient design and manufacturing of
`
`synthetic nucleic acids at a lower cost, with greater ease, reliability, and speed. Further, there is a
`
`need for a nucleic acid tool allowing for easy design and debugging of nucleic acid constructs.
`
`There is yet a further need to allow users of different skill
`
`levels,
`
`including users with little
`
`molecular biology knowledge,
`
`to design nucleic acid constructs
`
`for desired outcomes. The
`
`methods and systems described herein are useful to address these needs.
`
`SUMMARYOF THE INVENTION
`
`It is an object of the present invention to disclose a computerized system for designing nucleic
`
`acid sequences for gene expression comprising; (A) a server [103] for hosting a database [106]
`
`(B) a network connection [102] and (C) a computer readable medium [101] comprising
`
`functional modules including (i) a design module for enabling designing nucleic acid constructs;
`
`(ii) an interactive user interface module for visualizing biological information relating to design
`
`operations; (iii) a transaction module for purchasing a user-designed or pre-stocked nucleic acid
`
`constructs; (iv) a detecting module for detecting designed nucleic acid sequences comprising
`
`harmful sequences; wherein said system is operating in a method of: (a) visualizing biological
`
`information; (b) designing nucleic acid sequences; and (c) detecting and notifying when harmful
`
`sequences are designed; and (D) providing means for transactions regarding ordering and
`
`purchasing said synthesized nucleic acids.
`
`It is a further object of the present invention to disclose the system as defined above, wherein
`
`said computerized system is configured to be a software application and/or a web site running on
`
`a computerized device.
`
`It is a further object of the present invention to disclose the system as defined above, wherein
`
`said application is installed on a computerized device selected from a group consisting of: a
`
`telephone, a handheld device, and any suitable computerized device knownintheart.
`
`It is a further object of the present invention to disclose the system as defined above, wherein the
`
`nucleic acid is DNA and/or RNA.
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`PCT/IL2012/000326
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`It is a further object of the present invention to disclose the system as defined above, wherein
`
`said computer readable medium further comprises an access module to enable access for users to
`
`modules at different levels, access to different levels of functionality within a module and any
`
`combination thereof, said access defined by a predetermined variable.
`
`It is a further object of the present invention to disclose the system as defined above, wherein
`
`said predetermined variable is selected from a group consisting of: different pay grades, user
`
`type, and user skill-level and any combination thereof.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`design module is further configured to enable a user to edit said nucleic acid sequence and to use
`
`different predetermined controls in said design.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`controls are selected from a group consisting of: alteration of methylation sites, protein level changes,
`
`metabolic level changes and any combination thereof.
`
`It is a further object of the present invention to disclose the system as defined above wherein said
`
`editing of nucleic acid sequences comprises,
`
`for the relevant
`
`translation system, editing the
`
`incorporation of non-natural amino acids and other conventional molecular coding sequences, said
`
`sequences selected from a group consisting of heavy metals, markers, encoded data, any other
`
`suitable molecule knownin the art and any combination thereof.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`design module is further configured to enable a user to create a nucleic acid design from genetic
`
`clements selected from a group consisting of: transcription promoters, ribosome binding sitcs, gcncs,
`
`terminators, any othcr conventional genctic clements knownin the art and any combination thercof.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`design module is further configured to enable a user to stitch said nucleic acid constructs from
`
`building blocks that are available through said interactive user interface module.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`building block is at least one selected from a group consisting of a promoter, an open reading frame, a
`
`terminator, a Shine-Dalgarno sequence, and an expression system equivalentthereof.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`

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`WO 2013/030827
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`PCT/IL2012/000326
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`design module is further adapted for optimizing said designed nucleic acid construct according to
`
`various requirements.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`various requirements are selected from a group consisting of: optimizing codon usage, optimizing GC
`
`content, optimizing CpG content, avoiding problems associated with DNA motifs, avoiding problems
`
`associated with sequence repeats, avoiding problems associated with inverse complementary
`
`sequence repeats and any combination thereof.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`design module is further configured to utilize various computer-assisted methods for ascertaining an
`
`optimal codon sequence.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`optimal codon sequenceis in relation to the protein expression level in relevant expression systems.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`expression system is determined based on the nucleic acid sequence entered by a user.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`determining of said expression system is based on recognizing tRNA sequences.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`expression system is selected from a group consisting of: a cell, a cell-free system, in vitro system, a
`
`prokaryotic expression system, and a eukaryotic expression system.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`expression system is further selected from a group consisting of: bacterial cells, insect cells, SF9
`
`cells, Drosophila-Schneider cells, plant cells, yeasts, algae, plant expression systems and any other
`
`conventional system knownin theart.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`expression system comprises a system and/or a cell with a low level of methylation.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`design module further configured to matched said optimized codon to a codon that is most frequently
`
`or next
`
`to most frequently employed in a desired expression system for ensuring a general
`
`stabilization of the RNA and an optimal codon choice.
`
`4
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`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`design module further is configured to utilized a variety of suitable gene optimizer technology.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`designed nucleic acid is configured to be cloned into a vector thereby, it is operatively coupled with a
`
`suitable transcription control sequence and regulatory elements.
`
`It is a further object of the present invention to disclose the system as defined above, whercin said
`
`transcription control sequence compriscs a suitable constitutive or inducible promoter.
`
`The system of claim 1, wherein said database [106] further comprises dependency information for
`
`each genetic objects.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`computer readable medium further comprises a debugging module adapted for detecting errors in
`
`nucleic acid constructs.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`debugging module is further configured to compare designed nucleic acid constructs to said database
`
`[106] entries through sequence alignment.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`debugging module is further adapted for comparing said nucleic acid constructs in a designed module
`
`to the recipes for evaluation the successful nucleic acid sequence and the gene expression
`
`compatibility.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`debugging module is further adapted for determine the presence of errors with above predetermined
`
`threshold in said nucleic acid constructs.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`determine the presence of errors based on sequence alignment
`
`to said database entry, and the
`
`dependency information.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`debugging module provides output with alternative alteration of said designed nucleic acid construct.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`alteration is configured to fix a determinederrorin said designed nucleic acid construct.
`5
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`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`alteration is configured to be automatically accepted by said system and updated said nucleic acid
`
`construct.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`alteration is further configured to be given as an option to a user for him to decide whether to accept
`
`said alteration or not.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`debugging module evaluates the presence of necessary building blocks elements for prediction of
`
`gene expression level.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`debugging module evaluates said nucleic acid sequence of said building block for correctness,
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`debugging module evaluates the codon uses in said building block for prediction of expression
`
`compatibility level in a given expression system.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`evaluating gene expression compatibility comprises a success threshold.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`successful threshold set by a user.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`successful threshold is associated with a prediction of expressionlevel.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`computer readable medium further comprises a module for designating metabolic pathway to nucleic
`
`acid construct
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`designating metabolic pathway module is configured to annotate metabolic pathway descriptions to
`
`said designed nucleic acid construct.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`annotated metabolic pathway is obtained from a metabolic database comprises L.C. numbers related
`
`to genetic objects.
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`WO 2013/030827
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`PCT/IL2012/000326
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`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`F.C. numbers are obtained from a genome file related to said genetic object.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`designated metabolic pathway module is further configured to compare a portion and/or the entirety
`
`of said nucleic acid construct against genetic objects in the metabolic database.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`genetic objects comprises a threshold level of % similarity or identity to a nucleic acid construct
`
`sequences which annotated with a metabolic pathways, can be annotated with the same and/or similar
`
`metabolic pathway.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`designating metabolic pathway module is further configured to utilize a variety of suitable alignment
`
`module.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`suitable alignment module comprises an NCBI Blasttool.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`designated metabolic pathway module is further configured to apply a nucleic acid alignment
`
`algorithm to said submitted nucleic acid construct for finding sequences from said metabolic database
`
`with the highest alignment predeterminedscore.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`E.C. numberis associated with a picked or selected genetic object from said metabolic database can
`
`be assignedLo said submitted nucleic acid construct.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`E.C. numberfurther configured to assigned automatically.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`assigned E.C. numberis further configured to be stored in an associated file related to said genetic
`
`object.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`designated metabolic pathway module is further configured to designated metabolic pathwaysto said
`
`designed nucleic acid construct, via processing pathways related to an end and/or intermediate
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`product of the designed nucleic acid construct.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`designated metabolic pathway module is further configured to determine the functions of a selected
`
`enzyme, across multiple metabolic pathways and/or to offered replacement possibilities as options
`
`comprising one or more genes and/or gene products.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`designated metabolic pathway module is further configured to display catalytic activities, classified
`
`into groups, by using various visual icons associated with a gene/genetic object.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`metabolic pathways are further configured to be displayed automatically and/or upon user query.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`user query comprises a humaninteraction with a cursor.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`human interaction comprises actions selected from a group consisting of virtual pressing, sustaining,
`
`leveraging, pulling, pushing, opening, closing, capturing, grasping,
`
`sliding,
`
`rolling,
`
`turning,
`
`scratching, rubbing, shooting, stabbing, piercing, pinning, indicating, typing, directing or otherwise
`
`manipulating said cursor.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`database [106] is adapted for stocking sequences and/or previously ordered sequences.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`database is operably linked to the computerized systems.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`nucleic acid construct is
`
`configured to be checked against said database to determine whether
`
`portions or the entirety of said construct align to the entries of said database at above a predetermined
`
`threshold identity level.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`computer readable medium further comprises a module for optimizing said synthesis if nucleic acid
`
`constructs.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
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`optimize synthesis module is configured to optimized said synthesis of said nucleic acid sequence
`
`construct based on cost, ease, and/or speed.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`computer readable medium further comprises a module for generating synthesis protocols for nucleic
`
`acid constructs.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`module for generating synthesis protocols comprises an algorithm for automatically generated a
`
`construction protecol for said nucleic acids construct.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`algorithm is configured to generate a construction protocol with various criteria comprises, speed,
`
`and/or ease.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`module for generating synthesis protocols are further configured to insert said designed nucleic acids
`
`into an organism andto functionally express said designed constructs inside said selected organisms.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`interactive user interface is further configured to display various modules of the invention with
`
`associated functionalities.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`various modules are selected from a group consisting of nucleic acid design, error checking, codon
`
`optimization, metabolic product design, visual representations of biological information with dynamic
`
`zoom, nucleic acid synthesis, transacuions regarding ordering and/or purchasing synthesized nucleic
`
`acids, user review, ranking of nucleic acid constructs and/or any other conventional module with a
`
`functionality knownin the art.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`interactive user interface module comprisesplurality of resolution layers.
`
`It is a further object of the present invention to disclose the computerized system wherein said
`
`resolution layers are configured to display a biological information in a relevant way according to a
`
`predetermined chosen "zoom"level.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
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`resolution layers are further configured to correspond to differential visual representation of said
`
`biological information.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`interactive user
`
`interface module is
`
`further configured to dynamically switch said visual
`
`representation of said biological information in relation to a "zoom"level.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`biological information originates from said database [106].
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`biological information comprises genetic elements of said designed nucleic acid construct.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`visual representation of said biological information is related to an abstraction level.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`abstraction levels are pre-chosen to optimally represent said biological
`
`information in desired
`
`sufficiency.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`various abstraction levels configured to correspond to different
`
`levels selected from a group
`
`consisting of: organism, genome, system, metabolic pathway, protein, genetic sites, amino acids, or
`
`nucleic acid level detail.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`interactive user interface module comprises visual icons for enabling a user to switch to a desired
`
`abstraction layer,
`
`thereby, accordingly, a corresponding "Zoom" level
`
`is displayed on said user
`
`interface.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`biological information is configured to be "dragged" between zoom levels.
`
`It is a further object of the present invention to disclose the system as defined above, wherein said
`
`dragging operation adapted for executed a dynamic zoom function configured for switching a
`
`visualization of a genetic interface with an appropriate resolution, detail, and/or information.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`dynamic zoom function adapted for switching the displaying of a designed nucleic acid construct
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`between various views selected from a group consisting of: gene view, metabolic simulation view,
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`protein view, cellular view, organism view, organ view, complex organism view, for example yeast,
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`plant, animal, human, gender specific view or any other suitable view knownintheart.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`interactive user interface module is further configured to display said nucleic acid sequence constructs
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`in comparison to an average or most commonspecies sequence.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`interactive user interface module further comprises a representative icon.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`biological information further adapted to be selected and moved onto said representative icon for
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`representing the desired zoom level.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`interactive user interface module further configured to displayed a sequence variation in said nucleic
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`acid sequence within a species.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`sequence variation is configured to be display as a phenotype.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`interactive user interface module is further configured to displayed various views of said specific
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`nucleic acid sequence in comparison to object families, strains, genders, ethnicity, characteristic
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`groups and any other suitable comparison object knownin theart.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`representative icon is configured to be dragged and/or dripped into a design canvas.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`interactive user interface module further comprises various modules for molecular modeling and/or
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`simulations of protein structure,
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`molecular modeling and/or simulations of protein structure comprises operations selected from a
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`group consisting of moving, annotating, mutating and/or deleting operation.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`ordered and/or purchased nucleic acid constructs products comprise a kit comprising an isolated
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`synthetic preparation of a designed nucleic acid construct, and any other reagents and protocols for
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`the purpose of inserting and/or expressing the designed construct in a desired organism.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`transaction module comprises a marketplace of nucleic acid constructs available for purchase.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`marketplace populated by nucleic acid synthesis vendors and/or individual users.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`transaction module based on various criteria selected from a group consisting of availability of the
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`sequence, the synthesis method required to manufacture the nucleic acid construct, the uses of the
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`nucleic acid construct
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`transaction module is further configured to enable a user to submit a constructs with sequence
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`information, as well as any other relevant information selected from a group consisting of: gene
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`products, organism preferences, metabolic pathways or any other suitable information knownin the
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`art.
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`It is a further object of the present invention to disclose the system as defined above, wherein said
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`transaction module is further configured to enable a user to review and/or rank the constructs in said
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`marketplace.
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`It is a further object of the present invention to discl