Sample Non-Provisional Patent Application

8/2/2019 Sample Non-Provisional Patent Application

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TITLE

INTEGRATED DESKTOP SOFTWAREFOR MANAGEMENT OF VIRUS DATA

CROSS-REFERENCE TO RELATED APPLICATIONS[0001] This application claims the benefit of United States ProvisionalApplication No. 61/205,033, filed January 14, 2009, the disclosure of which isincorporated herein by reference.

BACKGROUND OF THE INVENTION[0001] This invention relates in general to a system and a method formanagement of virus data, including hepatitis C data.[0002] The hepatitis C virus (HCV), in particular, infects approximately 4million people in the United States and is the leading cause of chronic liverdisease. HCV-related end-stage liver disease is now a leading cause of deathamong HIV positive patients. HCV pathology includes fibrosis, cirrhosis andhepatocellular carcinoma. The hepatitis C virus is difficult to study and noteffectively treated with anti-viral drugs, with fewer than 50% respondingfavorably to the current therapies; and efficacious options are still years away.[0003] HCV is enveloped and contains a plus-strand RNA of 9 kb. TheRNA genome carries a single open reading frame (ORF) encoding apolyprotein that is proteolytically cleaved into a set of 10 distinct products (seeFig. 1, wherein diamonds designate cleavage points) which comprise the viralparticle and the viral replication machinery. The 5' untranslated region directstranslation of the HCV ORF via its binding of cellular ribosomes and proteins.HCV infects macrophages and hepatocytes and unlike the retroviruses, doesnot integrate into the host genome.[0004] Mutations accumulate in regions along the HCV genome constitutingmutation hotspots. These hypervariable regions are concentrated in five

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areas that include the NS5B protein, areas within and between the E1 and E2proteins, and in the core protein. HCV has six identified genotypes and over50 HCV subtypes that vary from one another in their nucleotide sequences by31-35%.[0005] HCV proteins mutate readily, leading to drug resistance. HCV is aremarkably successful pathogen. It has the ability to evade host immuneresponses, which it accomplishes by replicating rapidly and encouragingmutations via an error-prone HCV RNA-dependent polymerase that lacksproofreading capabilities. When HCV infects a patient, new variants (quasi-species, varying from one another in their sequences by 1-9%) arisecontinuously from the predominant infecting genotype during viral replication,resulting in hundreds of heterologous HCV genomes. The most fit of thesevariants are selected continuously in the replication environment on the basisof their replication capacities and selection pressures, including anti-viral drugpressures. At a given time during infection, the HCV quasi-speciesdistribution reflects a balance among the continuous generation of newvariants, the need to conserve essential viral functions, and positive selectionpressures exerted by the replicative environment. Thus, HCV infection setsup a complex problem for drug design, as scientists try to track HCV geneticvariation over time, between transmission of the virus, and after treatment withtherapeutic drugs.[0006] HCV infection presents a distinct set of analysis problems. The highmutation rate of HCV results in the accumulation of vast numbers of newgenetic sequences and associated biological data in the daily conduct oflaboratory research and clinical trials. Data management is a continuousproblem. Investigators currently rely upon homespun databases, genericsoftware products, and tools from public web repositories to sort, organize andanalyze their genomic and biological data. Table 1 (below) displays ninesteps that are routinely carried out to organize and analyze HCV sequence

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data (left column). The right column displays the corresponding programs ormanual steps that are commonly used to manage this data.

TABLE 1Routine Activity Software and/or Manual StepsGenotyping 1. MacVector

2. Mutation Surveyor3. BioEdit

Editing 1. Manually2. BioEdit3. Mutation Surveyor

Alignments 1. MacVector2. Mutation Surveyor3. BioEdit

Translation 1. LaserGene2. Mutation Surveyor

Mutation survey 1. Mutation SurveyorAnnotating 1. ManualPhylogenetic Analysis 1. MacVector

2. Public Databases (Los Alamos,Stanford)

Querying 1. LaserGene2. Public Databases (Los Alamos)3. In-house database

Graphics 1. Excel2. PowerPoint3. Illustrator4. Prism

[0007] In the Research Laboratory, a postdoctoral fellow will conductresearch and manage the data that is produced. Consider a project that

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involves a daily routine of selecting 100 HCV clones for sequencing per day(i.e. 500-600 clones per week). Each day the new sequences are stored on aserver or in folder files on computer desktops, and a series of routine actionsis performed on the sequences (Table 1). It is not unusual for the data fromseveral days work to accumulate and present extremely difficult tooverwhelming data-management problems that cause the project to bogdown.[0008] In the industry, trials often involve thousands of patients. Blood-draws on 1,000-2,000 patients/week require 1,000-2,000 sequences begenerated per week or about 200/day. Data management is an ongoingproblem. The routine actions performed daily on the sequences are similar tothose required in the research lab (see Table 1). One or several full timepeople are typically assigned to managing the data that accumulates.[0009] The high mutation rate of HCV results in vast numbers of newgenetic sequences and associated biological data in the daily conduct oflaboratory research and clinical trials with attendant serious data managementproblems. Investigators currently rely upon homespun databases, genericsoftware products, and tools from public web repositories to sort, organize andanalyze their genomic and biological data. These tools are often specific tocertain hardware or software configurations. These tools are not tailored tothe HCV genome and moving data from one program to the next is laborintensive, time consuming, and vulnerable to error.

SUMMARY OF THE INVENTION[0010] This invention relates to a system and a method for management ofvirus data, including hepatitis C data. The system may include desktopsoftware tailored for the rapid, efficient and flexible management of virus data,including HCV data. The system may make it easier for scientists toovercome data management problems. Moreover, the system may streamline

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the serious bottleneck of data management, significantly compressing the timebetween data collection and cure discovery.[0011] The system may be comprised of graphical-user interface (GUI) toolsand a data-storage and retrieval system (DSRS) that may be designedspecifically for analysis of a particular virus (e.g. HCV). It may also include acommercial relational database engine.[0012] The system may include an annotation tool which may simplify thecapture, storage and management of crucial experimental data points, andbring these user defined data points (annotations) into the same searchablecontext as those that are inherently systemic and structured.[0013] The system may further include alignment, phylogenetics andmutation analysis tools that may be specifically tailored to the mathematics ofthe virus's (e.g. HCV's) replication rate and its mutation genesis points (e.g.error-prone polymerase).[0014] The system may include a software architecture that is comprised ofthree tiers: a presentation (GUI) tier, a middleware (Domain) tier, and arelational database management system (RDBMS) tier.[0015] The alignment tool may be linked to a query tool and include a contigassembler for analyzing complete and partial genomic sequences. Thephylogeny tool may assemble alignments into evolutionary trees that cancolor-code and time-stamp the input sequences. A graphics tool may presentthe raw electropherogram data (traces), and assemble line and bar graphs toplot variables.[0016] The system may include additional tools for mutation tracking, reportgeneration and entropy measurement, as well as statistical routines andsecurity and installation packages.[0017] The system may merge informatics with basic research for rapiddiscovery. The system may aid in the rapidly developing market of HCVresearch. As a result, the system may greatly improve analysis capabilitiesand reduce data processing time. The system may also promote basic

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research in the field of bioinformatics and information sciences, and lead toenormous public benefit.[0018] The system may incorporate an N Tier structure that allows for thesoftware to be easily scaled across disparate hardware resources without theneed to retool. For example, individual tiers can be implemented on variousdifferent machines each running different operating systems, yet the overallsystem is still able to communicate and process the virus data effectively.[0019] Various advantages of this invention will become apparent to thoseskilled in the art from the following detailed description of the preferredembodiment, when read in light of the accompanying drawings.

BRIEF DESCRIPTION OF THE DRAWINGS[0020] Fig. 1 is a diagrammatic representation of the HCV genome.[0021] Fig. 2 is a diagrammatic representation of parts of an exemplarysystem for management of virus data.[0022] Fig. 3 is a diagrammatic representation of an exemplary tool set formanagement of virus data.[0023] Fig. 4 shows an exemplary application architecture.[0024] Fig. 5 shows an exemplary import tool.[0025] Fig. 6 shows an exemplary data manager window.[0026] Figs. 7 and 8 show a hierarchical folder and file structures.[0027] Fig. 9 shows windows of an exemplary annotation tool.[0028] Fig. 10 shows an exemplary editing screen.[0029] Fig. 11 shows an exemplary query designer window and anexemplary query results window.[0030] Fig. 12 shows exemplary windows of a query tool.[0031] Fig. 13 shows a diagrammatic representation of an exemplaryalignment tool.[0032] Fig. 14 shows a diagrammatic representation of an exemplary ContigAssembly Tool.

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[0033] Fig. 15 shows a diagrammatic representation of an exemplaryPhylogeny Tree Tool.[0034] Fig. 16 shows a diagrammatic representation of an exemplary tieredarchitecture embodiment.[0035] Fig. 17 shows a diagrammatic representation of an exemplary TraceViewer Tool.[0036] Fig. 18 shows a diagrammatic representation of an exemplary GraphTool.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT[0037] Now with reference to Fig. 2, there is illustrated an exemplary systemthat may address and overcome the major data-management problems thatare routinely encountered in working with viruses, such as HCV. The system10 may be comprised of graphical-user interface (GUI) tools 12 (e.g.,graphical icons and visual indicators that represent the information andactions available to a user) and a data-storage and retrieval system (DSRS)14, which may both be designed specifically for HCV analysis, or the analysisof other viruses. The system 10 may also include a commercial relationaldatabase engine 16 (e.g., a software component that may be used to create,retrieve, update and delete (CRUD) data). These components may enablethe integration, analysis and storage of genetic, biological, clinical andphenotypic data, and the capacity to query that data (see below).[0038] As shown in Fig. 3, the system may be comprised of various tools.The system shown includes an annotation tool 18, which may simplify thecapture, storage and management of crucial experimental data points, andbrings these user-defined data points (annotations) into the same searchablecontext as those that are inherently systemic and structured. Additionally, theannotation tool 18 may simplify the Data Manipulation Language (DML) forretrieving those data. As a result, the user may have unparalleled data-miningand analysis flexibility of high dimensionality data sets. Virus sequences,

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including HCV sequences, may be associated with many measured biologicalparameters, such as viral load, anti-viral inhibitor, cell line, length ofexperiment, liver enzyme profile, etc. Thus, the sequences may have a highdimensionality that is unique to the virus (e.g., HCV). These biologicalparameters may follow each sequence through storage and manipulation(currently HCV biologists attach and tend to these rider notes manually). Itshould be noted that alignment, phylogenetics and mutation analysis tools 20,22, 24 may be specifically tailored to the mathematics of a virus (e.g., HCV)replication rate and mutation genesis points (e.g. error-prone polymerase).The combination of these tools 20, 22, 24 in one place may greatly streamlinethe data management and manipulation problems so that the virologist canconduct his/her research in a more effective fashion.[0039] The alignment tool 20 may be linked to a query tool 26, which maybe an existing query tool. The alignment tool 20 may include a contigassembler 28 for assembling genomic sequence fragments into virus (e.g.,HCV) consensus sequences. The alignment tool 20 may suppress falsemutation predictions arising from technical error or misalignment, anditeratively improve alignments in the nucleotide and amino acid sequences(e.g., in the five HCV hypervariable regions (see Fig. 1) that are interspersedbetween the conserved regions). It may accomplish this with specializedsequence anchors and modified algorithms that may calculate distancesbased upon the cumulative mutations from baseline within these regions. Thephylogeny tool 22 may be provided for, among other uses, assembling thesespecialized alignments into evolutionary trees, and color-coding and time-stamping the input sequences, for example, based on desired result sets,such as according to quasi-species from single patient or clonal samples. Agraphics tool 30 may present the raw electropherogram data (traces), andassemble line and bar graphs to plot variables.[0040] Additional tools may be provided for mutation tracking, entropymeasurement and report generation. The system 10 may also include

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statistical routines 32, and security and installation packages. Together, thephylogeny tool 22, mutation tracking and entropy tools 34, 36 and statisticalprocedures 32 may quantify the degree of virus variation within and amongquasi-species sequences, for example, by calculating the nucleotide andamino acid sequence mutation profiles (diversity), entropy (complexity) andthe genetic distances (divergence). The mutation tracking tool 34 may belinked to the phylogeny tool 22 for determining the evolutionary rate of themutation types and the contribution of recombination to quasi-species diversityand to the adaptive evolution of the virus (e.g., HCV) under environmentalpressures.[0041] The statistical routines 32 may formulate output from the phylogenytool 22, mutation and entropy tools 24, 36 to compute virus (e.g., HCV)genetic variability. Used in conjunction with the annotation and query tools 18,26, these tools 32, 34, 36 may enable researchers to conduct crucial analysesregarding genotype sensitivity to anti-viral drugs, including: 1) investigatingquasi-species distributions and virus eradication, 2) comparing geneticheterogeneity among anti-viral responders and non-responders, and 3) askingwhether virus (e.g., HCV) quasi-species shuffle resistance mutations within oramong virus genes to increase diversity to drug resistant genotypes. Thestatistical routines 32 may also include formulas, for example, for calculatingthe covariance of the infecting genotypes to determine whether a change in anucleotide or amino acid at position A affects a mutation or recombination atposition B in a given sequence.[0042] The exemplary system 10 may be comprised of softwarecomponents that facilitate the storage, integration and analysis of genetic,clinical and phenotypic data and have the capacity to query that data. Forexample, as illustrated in Fig. 4, the software architecture may be comprisedof presentation, middleware/logical, and database tiers 38, 40, 42 withinteraction object layers. For example, these tiers may be comprised of GUI,middleware, and data components. GUI components may include forms (e.g.,

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windows forms) that may be served to the user from a presentation tier as GUItools 12 with which the user may interact. GUI components may take inputfrom the user and display results. Middleware components may house theprocessing logic (e.g., methods) used by the system 10 to process input andreturn output to GUI components (e.g., GUI objects). Middleware components(e.g., middleware objects) may interact with the database components, forexample, by preparing and transmitting data for storage and retrieving datafrom the database components. The database tier may include a RelationalDatabase Management System (RDBMS) 44 for persistent data storage, anda data model. The software architecture is described in greater detail in thedescription herein below.[0043] Entering sequences may be easily accomplished via multiple optionsduring a user session. Virus sequences may be entered into the system 10,for example, through any suitable data entry tool capable entering virussequences or virus sequence data. It should be appreciated that sequencesmay be submitted to the system 10 in bulk using a bulk sequence import tool.An exemplary import tool 45 is shown in the center of Fig. 5. Import tool maybe configurable to allow incoming sequences to be left alone as a rawimported data or be automatically processed in some way, such as beingautomatically translated, or being automatically identified. A suitable tool maybe designed to accept genetic sequences as individual files, FASTA formatfiles, or any other suitable data sources. This permits live import of data froma sequencing device or machine. The sequencing machine can be directlyconnected to the system or software, or the software can be incorporated inthe sequencing device or machine, without generating files. The tool may alsobe designed to accept various types of sequences, such as nucleic acid (ntd)or amino acid (aa) sequences. The user can choose to genotype, translateand identify complete and partial virus (e.g., HCV) proteins using a sequenceidentifier (see Fig. 5). An exemplary sequence translator tool may translatenucleic acid into amino acid sequence data. An exemplary sequence identifier

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may be in the form of a tool comprised of algorithms used to identify all knownvirus (e.g. HCV) genotypes and subtypes. Upon sequence entry, the system10 may automatically calculate the net charges of proteins and tally allglycosylation and phosphorylation sites. Genotyping and translation may bepresented as options to the user.[0044] In Fig. 6, there is illustrated an exemplary data manager tool (e.g.,window 46), which may be seen by a user after entering sequences. The datamanager window 46 may comprise a record explorer 48 that may include aflexible leaf and node/tree type organizer 50 that may allow users to easilymanage their sequence data. Users can create hierarchical file and folderstructures (see Figs. 7 and 8) into which they may load various objects,including but not limited to sequence banks, alignment results, traces, andquery results.[0045] The exemplary system 10 may further include a sequence viewertool 51 (e.g., a display and editing tool that allows users to view storedsequences). Users may select single or multiple banks of sequences 52 fordisplay. Once displayed, various options may be available for working withselected sequences, such as editing, annotating, constituent protein view ornucleotide region view. New sequences may be added to a target sequencebank or multiple sequences may be chosen for alignment. This is the generalworkspace where users may manipulate and view the sequences storedwithin their sequence banks. The system 10 may allow for various tools to beutilized from within this and other workspaces.[0046] By highlighting a sequence in the sequence viewer 51 (as shown inFig. 6), the user can view the individual proteins identified within thatsequence in the region/protein viewer screen 53 (shown in the bottom panel ofthe data manager window 46 when in Fig. 6). The region/protein viewer 53may be capable of displaying nucleotide and or protein sequences assegmented into their constituent proteins or regions, respectively. Singlesequences may be chosen from the sequence viewer for display within this

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tool. Users may toggle between protein and nucleotide region views. Thesystem 10 may permit nucleic acid coding regions and proteins to be relatedto the raw data. The user can choose various options from menu items forsequence editing, translation, genotyping, annotating, saving or deleting, aswill become more apparent in the description below. Although the datamanager 46 may function as a graphical user interface (GUI), whereby usersmay interact with the system, a non-graphical data manager may beimplemented separately or in combination with the GUI.[0047] User-defined annotations can also be linked to single or multiplesequences with the annotation tool 18 (see the annotation screen 54 to theupper right of the data manager window 46 when in Fig. 6). The annotationtool 18 may act as a user defined data submission tool that allows users toview and attach data entries to sequences for reference. Standard and user-defined annotations may be linked to the sequences at anytime during asession. The annotation screen 54 may allow users to create definitions forvalues or text representing clinical, experimental, and/or biological data theywould like to link to their genetic data. This user-defined annotation systemmay allow researchers to easily comply with patient confidentially and HIPPAstandards because they may choose how they store their collectedinformation.[0048] The user can select to add annotations to sequences at anytimeduring a session. Annotations already defined in the system may be attachedto a sequence for selection items as shown the Add New Annotation window55 (the right panel when viewing Fig. 9). New annotations can be created inthe Annotations Definition Manager 56 (the lower panel when viewing Fig. 9).The user may enter the annotation name, defines the type of annotation in adrop-down menu and can choose whether the annotation is restricted tocertain values. Exemplary embodiments of the system 10 may allowannotations to take virtually any form, including text, numbers, images,hyperlinks, file associations, or other useful data. The ability to define an

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annotation with great precision allows for complex searches using the querytool 26.[0049] Users may choose the sequences they wish to annotate and do sowithin the annotation tool 18, which may be displayed next to the sequenceviewer for convenience. Annotations are searchable. The AnnotationsDefinition Manager 56 may allow users to pre-define labels and associateddata types for customized annotations (e.g. patient 10, biopsy type, sequencedates, etc.). The annotation tool 18 may also allow users to customizefunctionality, e.g. to find and return special patterns in certain positions withina sequence. The annotation tool 18 may further allow users to view, add new,and edit existing annotations for individual sequences or sequence sets.[0050] Clicking on any of the edit sequence menu items, from the edit menu57 (shown in Fig. 6), or the edit tool icon (not shown), may reveal the intendedsequence for editing, translating or re-translating, genotyping and saving. Anexemplary sequence editor tool 57 is shown in Fig. 10. The sequence editingtool 57 may allow a user to add and edit sequence data. The "next dash"button 58 may jump the cursor easily from dash to dash, eliminating manualediting repetition. This window may also enable single sequence entry, bysimply pasting a FASTA-formatted sequence (ntd or aa) into the appropriatewindow. The FASTA sequence label may be automatically parsed into a"Label" box 59.[0051] The linkage of virus (e.g., HCV) genomic, clinical and experimentaldata provides the system 10 with advanced query power. An exemplary querytool 26 is shown in Figs. 11 and 12. The query tool 26 may include a querydesigner window 60 and a results or reporting window 62. The designerwindow 60 allows the user to select attributes, such as treatment response,number of glycosylation sites, and sequence charge. Easily designed queries,directed at relational data sets, may aid in identifying and correlating specificgenetic virus changes with therapeutic, biological, demographic, and clinicalfeatures. Users can isolate sets of information via user-defined genetic

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characteristics (modify searches, region ID) or via sequence-associatedannotations.[0052] Query results may be reported in the results window 62. The resultswindow 62 may provide an easy view of retrieved data. In the exampleshown, the results window 62 shows treatment duration, response outcomeand number of glycosylation sites located for the E1 and E2 domains. Queryresults may be aligned with the alignment tool 18 or run through another toolin the system 10 for advanced analysis. Using the annotation tool 18, a usermay search and annotate their sequences for these special post-translationalmodified sites, which enabled this exemplary query.[0053] From the results window 62, the user may ask for the calculations ofthe percentages of variation at any position in the alignment. Right clicking ona sequence may bring up the sequence editor tool 52 so that either thesequences or annotations, or both, may be edited. The results window 62may be exported into various formats, such as an Excel file, or sent to thealignment tool 20 (e.g., by right clicking).[0054] The query tool 26 may allow users to mine their sequence datalimited only by their annotations. This tool may be embodied in a user friendlypoint-and-click interface for defining query parameters and output fields tofacilitate reporting and mining of sequence data. Users may choose from listsof fields inherent in the default data structure, but may also search customfields (annotations) as defined by the user in the annotation tool 18. Queryresults may be displayed in various formats, such as grid format and may beexported in various formats, such as CVS or FASTA, as appropriate.[0055] An exemplary use of the query tool 26 is as follows. A user maywish to examine a preliminary correlation between viral infectivity and immunefunction. Viral envelope proteins play key roles in host cell tropism, infectivityand immune response. A positive charge level on HCV E2 may enhance viralinfectivity, the number of proline residues impact E2 alpha helix formation and

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thus viral entry, while lowered CD4+ counts suggest a declining immunefunction and progression of HCV infection.[0056] To examine the aforementioned correlation, the user may query thesystem 10 to i) locate all E2 sequences with an aa charge greater than ( 4,CD4+ counts between 1 and 55 and a proline count >20 (see the operatorselection panel 64 in Fig. 12) and ii) retrieve all E2 aa sequence data, E2charge and glycosylation counts, patient ID numbers and CD4+ counts in theresult set. This simple query may produce a result set (shown in the resultswindow 62 in Fig. 12) that allows the researcher to correlate sequencesassociated with cell tropism to a disease progression parameter. All motifsand special region counts, such as glycosylation and phosphorylation sites,can be highlighted, for example, using the highlighting tool 66 (shown as thelower panel in Fig. 12).[0057] Queries can be saved and annotated as needed. The alignment tool20 may be linked to the query tool 18, enabling all associated query attributesto be highlighted in the alignment.[0058] Now with reference back to Fig. 4, there is illustrated middleware 40(i.e., a domain layer), which may be comprised of a plurality of logical layers.In an exemplary system 10, the middleware 40 may comprised of two layers.One is for processing domain logic and is called "business rules" 68. Thislogical layer 68 may reside between the presentation and data access layers70 and may be responsible for processing requests from and to thepresentation layer and from and to the data access layer 70. All classes thatexist in the business rules 68 may have complementary classes in the dataaccess layer where applicable. The data access layer 70 may exist betweenthe domain logic layer 68 and the RDBMS 44 and may be called "DataAccess." The data access layer 70 may include all classes responsible forrequesting data from and submitting data to the RDBMS system 44. Allclasses that exist in the Data Access layer 70 may have a complimentary

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class in the Business Rules layer 68 as well as complementary tables in thedata model 72, described herein below.[0059] A Database (RDBMS) 44 may be used for persistent storage ofapplication data. It may comprise a third party relational databasemanagement system (RDBMS) and a data model 72. The data model 72 maydefine table entities whose interdependencies are defined via primary andforeign key relationships. The model 72 may contain entities that containsequences, annotations, reference sequences and supplemental data(genotype lookups, annotation data types, etc.). An exemplary RDBMS 44may use a freeware version of Microsoft SOL Server 2005 express.[0060] An exemplary system 10, as described above, may utilize thefollowing technology.

Software:Application Framework: Microsoft ASP .NETLanguages:

VB .Net: View and Presenter objectsC# .Net: Business Rules and Data Access objectsC++: 3rd party algorithm integration

Windows Forms .NET: PresentationT-SOL: Tree View data harvesting stored proceduresXML: Tree View presentation schemaSOL: DDL and DMLRDBMS (Microsoft SOL Server 2005 Express)IDE (Microsoft Visual Studio .NET 2005)

Hardware:Memory: 2g DDL RamCPU: 1g PentiumHard Drive: 80g 7800 rpm Seagate

[0061] As mentioned above, the system 10 may use an N Tier architectureapproach comprised of presentation, middleware, and relational database

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system (persistent data store) tiers. The presentation tier 38 may becomprised of view components, such as the GUI tools 12 (e.g., windowsforms), and presenter classes (e.g., event handlers and logical applicationprocessors). The middleware tier 40 may be comprised of main domainlayers, such as domain logic (i.e., business rules) 68 and data access 70. Thescalability implied by this architecture approach may be leveraged so that theexemplary system 10 may be scaled to load, without the need to retool. Thus,the system 10 may be embodied across multiple computers and multipleoperating systems easily, without the need to substantively redesign thesystem 10. The system 10 may be developed using a model view presenter(MVP) design pattern. The system software application may be written chieflyin C# .NET (or other suitable language), and may be split into three layers,including UI (view), application (presenter), and domain (model) layers. TheUI layer may present windows forms controls to the user and may delegateprocessing needs, for example, via event handlers and requests, tocorresponding objects of the presenter. The view layer may contain noprocessing logic related to domain or application layer objects. Applicationlayer classes may handle communications to and from corresponding viewclasses via interface. Event handlers for corresponding view objects mayreside at the presentation layer. Presentation layer objects may handle thedelegation of application workflow, validation of user inputs, messaging, anddomain layer interface requests. The application layer may also receiverequests from ancillary background services for automated testing routinesindependent of the view. The domain layer may include all classes related tothe processing of logical requests regarding information handed down fromthe application layer or passed back via requests from persistent data store.Corresponding objects at the domain and presenter layers (e.g., algorithmicalignment processing and resultant list objects, slated for view layer display)may interface bi-directionally.

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[0062] The following section of this disclosure details exemplary systems 10and exemplary tools 17.[0063] An exemplary sequence alignment tool is generally indicated at 20 inFig. 13. The sequence alignment tool 20 may enable users to arrange theprimary DNA, RNA or protein sequences to identify regions of similarity thatmay be a consequence of functional, structural, or evolutionary relationshipsamong the sequences. Alignments may tend to be less accurate with rapidlymutating viruses, such as HCV. Thus, algorithms may be included to alignany hypervariable regions (e.g. five shown for HCV) separately from theinterspersing conserved sequences along the genome, and calculatingdistances based on the cumulative scores of the combined mutation profile ofthe infecting genome(s).[0064] The sequence alignment tool 20 may allow a user to: a) choosesequences from a navigation window; b) have the system 10 automaticallydifferentiate between pair-wise and multiple alignment choices based onwhether or not the user selects two or more sequences, respectively; c)choose from a variety of appropriate algorithms, scoring matrices, and gappenalty values; d) choose to suppress false negative mutations by selectingfrom a menu of polymerases purchased from biotech companies (e.g.,TaqMan) (an algorithm may incorporate the error rate of the polymerase intothe formula); e) select to consider all or a subset of the five hypervariableregions apart from conserved areas for assembly; f) have the program colorcode various disease specific data points (e.g., glycosylation, phosphorylation,mutation, or user-defined decoration); g) view, save, annotate and exportresultant alignments; h) assemble, edit and save alignments or contigs; and/orperform other related tasks.[0065] Custom windows forms user controls, logical domain classes, anddatabase objects to address these tasks may be created. Users may selecteach sequence in the sequence viewer they wish to align. Once more than asingle sequence has been selected in the sequence viewer, an alignment

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button may be enabled atop the sequence viewer, that when activated maycause a horizontal split container panel to rise and load an instance of acustom user control that may be devoted to collecting alignment parameters.This control may be called, for example, the "alignment designer."[0066] The alignment designer 73 may comprise a split container, whichmay be subdivided into two panels, for example, left and right panels. The leftpanel may contain a list control which may be populated with a list of labelsassociated with the sequence viewers' selected sequences. To the right ofthe list control, image button controls (e.g., up and down arrow buttons) maybe presented to allow users to reorder sequences at will (these may also allowthe user to specify the order in which the sequences may appear in theoutput). The right panel may contain a list of alignment algorithms from whichthe user may choose. The list of algorithms may be populated with the namesof various local and global, pair-wise and multiple, protein and or nucleotidealignment algorithms. The list of algorithms may be populated in accordancewith the number of sequences to be aligned (e.g. if the user chooses twosequences, the user may be presented with a list of the names of anyavailable pair-wise alignment algorithms, whereas, if the user chooses morethan two sequences, a list of multiple alignment algorithms may bepresented). Once an algorithm is chosen from the list, a list of parameteroptions may appear below an algorithm drop down list control that may allowusers to supply parameters, pertinent to the requirements of the algorithmchosen (e.g., gap penalties, scoring matrices, etc.). Below the algorithmicparameter values, a list of mutation type-specific or other user-definedparameters, such as color coding indicator controls, may be presented, suchas in the form of drop down lists with conjoined color picker controls. Theseparameters may be used by the application to highlight important changes inthe RNA and amino acid sequences in the resultant alignment display. Suchmutations may include an RNA mutation that confers a functional change tothe corresponding amino acid, such that the mutation newly renders the amino

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acid a target of post-translational modification (e.g., glycosylation orphosphorylation site), or the cause of structural changes in the protein. Oncethe user has adequately supplied all parameter values, a button entitled"align" may be enabled.[0067] When the user activates this "align" button, the parameterinformation may be passed to a controller interface 74 through which domainlogical processors devoted to conducting the alignment may be invoked. Tocompliment this process, a progress indicator control window may be created.The progress indicator control window may contain a progress indicator bar, alabel control (which may populate with text regarding state of the process) anda cancel button, that when activated, may interrupt and dispose of the currentprocess. A results control 76 may be created. The results control 76 maycontain a display of the output of the tool, such as a DataGridView control,and buttons, such as a cancel button and a save button. This control willdisplay the aligned sequences to the user. The user may then activate thecancel button to close the control (thus returning the user to the parametercontrol) or activate the save button to retain the alignment data. A control maybe created to compliment the save action. This control may contain a textboxcontrol that allows the user to name the alignment and navigation means,such as a browse type dropdown list, to allow the user to point to the folder inthe record explorer where the alignment record will reside and be presentedas an icon with the label data point supplied by the user. The user may havethe ability to associate custom annotations with alignment containers and mayhave the ability to search for those objects via the query tool, as needed.[0068] An exemplary contiguous assembly tool ("contig assembly tool") isgenerally indicated at 28 in Fig. 14. The contig assembly tool 28 may be anaspect of the alignment tool 20 or be embodied separately. The contigassembly tool 28 may assemble fragment data from sequencing projects ofany size, from several to tens of thousands of fragments, into a singleconsensus sequence. The contig assembly tool 28 may be designed to allow

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a user to: a) submit sequence fragments to the alignment tool 20 for multiplealignment; b) submit a reference sequence for the contig assembler to alignfragments against; c) design a contig assembly project to identify and removeunreliable data, including poor quality 3' or 5' ends, sub-minimal length reads,and vector sequences; d) save the resultant consensus sequence; and e)recall the saved sequence for parameter manipulation and re-assembly;and/or other related tasks.[0069] Custom windows forms user controls, logical domain classes, anddatabase objects to address these requirements may be created. Users mayselect a set of fragments from a sequence bank object in the record explorer48 that may, in turn, populate the sequence viewer 51 with the fragmentsstored, therein. Users may also choose a sequence to use as an alignmentreference. Users may select each sequence in the sequence viewer 51 theymay wish to use for contig assembly tool 28. Once more than a singlesequence has been selected in the sequence viewer 51, a contig designerbutton may be enabled atop the sequence viewer 51, that when activated maycause a horizontal split container panel to rise and load an instance of acustom user control that may be devoted to collecting contig assemblyparameters. This control may be called "Contig Designer". The contigdesigner 78 may use much of the same features as the alignment designertool; this is because contigs may first be aligned to a reference sequencebefore being consolidated into a contiguous sequence.[0070] The contig designer 78 may include a split container, which may besubdivided into panels, for example, left and right panels. The left panel maycontain a list control which may be populated with a list of labels associatedwith sequence viewers, selected fragment sequences and referencesequence. To the right of the list control, image button controls (e.g., up anddown arrow buttons) may be presented to allow users to reorder sequences atwill (these may also allow the user to specify the order the sequences mayappear in the contig preassembly, alignment (scan) output). The right panel

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may contain a list of multiple alignment algorithms from which the user maychoose. Once an algorithm is chosen from the list, a list of parameter optionsmay appear below the algorithm drop down list control that may allow users tosupply parameters, pertinent to the requirements of the algorithm chosen(e.g., gap penalties, scoring matrices, etc.). A default configuration for optimalcontig preassembly alignment may be configured (e.g., no penalties for endgaps, high internal gap costs, short match with high score/residue). Below thealgorithmic parameter values, a list of checkboxes may be presented. Thesecheckboxes may be associated with additional preassembly options for theuser to choose from, such as a) automatic removal of vector sequence(s)(strongly recommended when using Sanger data); b) removal of contaminantsequence(s); c) identification of repetitive sequence(s); d) automatic 5' and 3'end trimming; e) manual end setting; f) allowing the assembler to optimize theorder in which it assembles fragments; and/or other related options. Once theuser has completed the assembly design, a button entitled "Assemble" may beenabled. When the user activates the "Assemble" button, the parameterinformation may be passed to a controller interface 74 through which domainlogical processors devoted to conducting the multiple alignment andsubsequent consensus sequence assembly may be invoked. To complimentthis process, a progress indicator control window may be provided. Theprogress indicator control window may include a progress indicator bar, alabel control (which may populate with text regarding state of the process) anda cancel button, which when activated may interrupt and dispose of theassembly process. A results control SO may be provided. The results controlSO may include a display of the results of the contig assembly tool 2S, such asa text box, DataGridView control, as well as functional buttons, such as acancel button and a save button. The text box may be populated with theconsensus sequence. The text box may be scrollable (e.g., left and right).The DataGridView will contain all aligned sequence fragments. The user maythen activate the cancel button to close the control (thus returning the user to

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the contig designer) or activate the save button to retain the results of thecontig assembly tool 28. A control may be provided to compliment the saveaction. The control may include a textbox control that allows the user to namethe alignment and a navigation means, such as a browse type dropdown list,to allow the user to point to the folder in the record explorer 48 where theassembly record may reside and be presented as an icon with the label datapoint supplied by the user. The user may have the ability to associate customannotations with alignment containers and may have the ability to search forthose objects via the query tool 26, as needed.[0071] An exemplary phylogeny tool is generally indicted at 22 in Fig. 15.The phylogeny tool 22 may assemble the specialized alignments that considerthe hypervariable regions into evolutionary trees, and that may color-code andtimestamp the input sequences according to desired aspects, such as quasi-species from single patient or clonal samples. An exemplary phylogeny tool22 may allow a user to: a) design and conduct a multiple alignment asdescribed by the alignment steps disclosed above; b) color code sequences orregions of sequences for easy tracking of quasi-species by mutation type orregions under selective pressure in a single patient or clone from the tree; c)create and graphically display rooted phylogeny trees; d) save resultant treesin a discernable format, such as the PAUP (*.pau or *.nex) format; and/orother related tasks.[0072] Custom windows forms user controls, logical domain classes, anddatabase objects to address these requirements may be created. Users mayselect sequences from the sequence viewer 51 for alignment design (asdescribed above). The right hand split container of the alignment designer 73may include a button control called "optimize for phylogeny." When a userclicks this button, default alignment options may populate the designer's inputparameters, choosing the alignment algorithm best suited for the phylogenytree build (e.g., ClustalV) and automatically populating associated parametercontrols with values optimized for phylogeny building (see the phylogeny

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optimizer 82 in Fig. 15). Additional parameter controls may be created andrendered (such as color pickers for easy tracking of quasi-species). After allrequired alignment parameters are populated, a button called "Build Tree"may be enabled. When the user activates the "Build Tree" button, theparameter information may be passed to a controller interface 74 throughwhich domain logical processors devoted to conducting the multiple alignmentand subsequent tree assembly may be invoked. To compliment this process,a progress indicator control window may be created. This control may containa progress indicator bar, a label control (which may populate with textregarding state of the process) and a cancel button, that when activated, mayinterrupt and dispose of the tree build process. A custom user control 84called "tree view" may be created. This control 84 may instantiate a customcontrol that may render the results of the tree build process. Windowsdrawing objects or other similar means may be used to accomplish thecreation of this control output. Color coding options may display inaccordance with user input parameters (where applicable). Options may beavailable to retain and save the results of the tree build process.[0073] Corresponding domain objects may be created, for example, in C#,to facilitate the processing of the various tools. Domain logic may besubdivided into categories, for example, business rules 68 and data access70. Corresponding objects related to each portion of the various tools may becreated at the domain level, for example, one for business rules 68 and theother for data access 70.[0074] In the exemplary system generally indicated at 10 in Fig. 16, abusiness rule object named "Alignments" may be created to handle requestson behalf of the complimentary application layer object, which may also benamed "Alignments.". A data access object may be created named"AccessAlignments" to handle database interaction on behalf of the"Alignments" domain object requests. The "Alignments" object may becomprised of properties to get and set the alignment designer input, properties

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that may contain the results of an alignment, methods for conductingalignments or methods that interface with third party components whichprocess alignments and return results. The "AccessAlignments" object mayinclude methods that contain RDBMS brand specific DML which may facilitatethe saving and retrieval of persistent input to and output from the RDBMSengine 44. A business rules object named "ConfigAssembler" may becreated, to handle requests on behalf of the complimentary application layerobject, also called "Alignments". A data access object named"AccessConfigAssembler" may be created to handle database interaction onbehalf of the "ConfigAssembler" domain object requests. The"ConfigAssembler" object may be comprised of properties to get and set theContig designer input, properties that may contain the results of contig projectexecutions, methods for conducting alignments or methods that interface withthird party components which process alignments and return results, andmethods to assemble the contiguous consensus sequence. The"AccessAlignments" object may contain methods that may contain RDBMSbrand specific DML which may facilitate the saving and retrieval of persistentinput to and output from the RDBMS engine 44.[0075] A supporting data model 72 may include multiple entities. In anexemplary system 10, the data model 72 is comprised of four entities. Thefirst entity may be called "sequence alignment" and may be used to store theheader record of the sequence alignment. It may include the following fields:primary key/identity field (UIP), a name field (label), and a parameter/headerfield (params). The second entity may be called "alignment sequence" andmay store pointers to the individual sequences that make up the alignmentand the sequence as aligned. It may include a primary key/identity field (UIP),a foreign key field (seq_align_uid), the UIP of the sequence row as stored inthe sequence table (sequence_uid), and a field to contain the sequence as itappears in the alignment results. The third entity may be a header record forthe contig assembly session and it may include a primary key/identity field

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(UIP), a name field (label), and a parameter/header field (params). The fourthentity may contain the contig alignment results and it may have the followingfields: a primary key/identity field (UIP), a foreign key field(contig_assembly_uid), the UIP of the sequence row as stored in thesequence table and a flag that may be used as a tri-state indicator to let thesystem know whether or not the sequence is a fragment, contig, or reference.[0076] In an exemplary system 10, a business rule object named"PhyloTree" may be created, for example, to handle requests on behalf of thecomplimentary application layer object, also named "PhyloTree". A dataaccess object named "AccessPhyloTree" may be created to handle databaseinteraction on behalf of the "Phylotree's" domain object requests. The"PhyloTree" object may be comprised of properties to get and set thealignment designer input, properties that may include the results of analignment, methods for conducting alignments, and methods for producing thephylogenic tree (e.g. neighbor joining). The "AccessPhyloTree" object mayinclude methods that include RDBMS brand specific DML which may facilitatethe storage and retrieval of persistent data to and from the RDBMS 44.[0077] A supporting data model 72 may comprise multiple entities. In anexemplary system 10, the supporting data model 72 may comprise twoentities. A first entity may be called "phylo sequence alignment," and it maybe used to store the header record of the initial sequence alignment and theresultant tree. It may contain the following fields: primary key/identity field(UIP), a name field (label), an alignment parameter/header field(alignment_params), and a second parameter/header field (phylo_params).[0078] A second entity may be called "phylo sequence" and may storepointers to the individual sequences that may make up the initial alignment. Itmay contain a primary key/identity field (UIP), a foreign key field(seq_align_uid), the UIP of the sequence row as stored in the sequence table(sequence_uid), and a field to include the sequences as they appear in thepreliminary multiple alignment results.

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[0079] Graphics tools may be developed to aid the researcher in theanalysis of HCV data. Graphics tools may present the raw electropherogramdata (traces), and assemble line and bar graphs to plot up to two variables.Graphics tools may enable a user to store and view trace files associated withtheir sequences and to have the application assemble line and bar graphs toplot up to two variables.[0080] Custom user controls may allow users to accomplish these tasks. Afirst control may be a trace viewer, shown in Fig. 17, and a second may be agraphical chart generator, shown in Fig. 18.[0081] A windows forms control may allow users to view chromatogramtrace files, associated with sequences submitted to the system. Thesequences edit and add tools may be enhanced to allow the storage of tracefiles. In an exemplary system 10, a button control called "add trace file" maybe added to the sequence edit control 51. When a user activates this button,a windows file system dialogue window may appear, prompting the user tochoose the location of the trace file from the local file system or over thenetwork. Once the user locates the trace file to be associated with thesequence, the user may select that file. Upon doing so, the file systemdialogue window may close and the trace file path may be supplied to adomain method which may pass the contents of the file and the full path intothe properties of the sequence to be saved. The user may then activate asave button to save the data; the sequence may be updated and the editsequence window may close. The sequence row as represented in thesequence viewer 51 may be update to include an icon, indicating that thesequence record includes a corresponding trace file. When the user activatesthis icon, the trace file viewer window may appear.[0082] A custom user control called "trace view" 86 may instantiate acustom control that may read and interpret the trace file. Windows drawingobjects maybe used to accomplish the creation of this control output. Classesto interpret each type of supported trace file (such as ABI and SCF) and paint

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its sequence (color coded, such as by nucleotide) and corresponding tracegraph (color coded, such as by nucleotide) may be created. Users may beable to scroll left and right to view the trace in full.[0083] Custom window forms controls may allow users to view graphs,related to specialized, virus (e.g. HCV) specific custom annotation valuesassociated with sequences in the system. Check box controls may be addedin the annotation explorer panel, associated with particular annotations thatmay be common to all sequences in the view. These annotations may sharea common data type. Once the common annotations are selected, a radiobutton control with two list items may be enabled, one for example labeled"line graph", the other labeled "bar chart" and a button control entitled "viewgraph" may be enabled. Upon selecting either a radio button and activatingthe "view graph" button, a new window called "graph viewer" may pop up.This window may contain a custom image control that may display theresultant graph image, rendered by the system in accordance with the datapoints supplied by the common sequence annotation record values and anexport button to allow the user to save the resultant image to the file system(for export to other programs and formats, such as Excel or PowerPoint).[0084] Corresponding domain objects in C# may facilitate the processing ofthe abovementioned tools. Domain logic may be subdivided into categories,for example, business rules 68 and data access 70. Corresponding objectsrelated to each tool may be created at the domain level, for example, one forbusiness rules 68 and the other for data access 70. In an exemplary system10, a business rule 68 object named "Trace" may be included to handlerequests on behalf of the complimentary application layer object, also named"Trace." A data access object may be named "AccessTrace" may handledatabase interaction on behalf of the "Trace" domain object requests (namely,to retrieve the binary trace data from the sequence record). The domain logic"Trace" object may be comprised of properties to get and set trace viewparameter (such as, color coding of nucleotides and sign waves) and methods

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to introspect the binary data points and interact with windows drawing objectsto create the visual trace output. The "AccessTrace" object may includemethods that contain RDBMS brand specific DML which may facilitate thesaving and retrieval of persistent input to and output from the RDBMS engine44 related to the trace file associated with a sequence. A business rule objectmay handle the interpretation of the graph data, and to render the results ofthe process into a bitmap file for display and export.[0085] There is a fundamental void of understanding about how thenumerous viral (e.g., HCV) variants impact the host's genomic response. Togauge this response, researchers examine the infected host genome at thetranscription level by analyzing their gene expression profiles using microarraytechnologies. The system 10 may incorporate a database for microarray datafrom, for example, 50,000 transcripts and can link the viral (e.g., HCV)sequences directly to a host microarray profile. The system 10 may alsoenable normalization of microarray chip data generated from differentchemical platforms (e.g. two-color systems, lithographic synthesis, etc). Theviral (e.g., HCV) protein and microarray files are linked with a common IDnumber. The system 10 may maintain the relational hierarchy with ongoingexploration capabilities. Also, the system 10 may implement a lateral linkageability so that the user has the option of linking or not linking subsequentexpression and sequence data.[0086] A genotyping tool may identify the genotype and serotype of anincoming sequence by comparing (e.g., three) small nucleotide domains in(e.g., three) regions (e.g., "C/E1/NS5B/5'UTR" in HCV) in agenotype/serotype-specific viral reference sequence with an incoming virusgenome. This genotyping strategy, based upon the conservation findings ofMurphy et al. (2007) it is highly accurate, distinguishes all known virusserotypes (e.g., n=77 in HCV) and represents the latest in virus identificationover all other methods. The genotyping tool may use a sequence orientationschema that relies upon the conserved regions for orientation and

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identification to one domain (e.g., NS5B in HCV), then another domain (e.g.,C/E1 in HCV) and until finally, the last domain (e.g., 5'UTR in HCV). Thismulti-tiered (e.g., three tiered) validation approach may ensure approximately90% accuracy of genotype/serotype identification. This tool may be readilymodifiable to genotype and serotype other viral sequences as well.[0087] It is understood in the art that any above mentioned usage ofwindows form controls may be enacted by various other similar programmingmeans and on other operating platforms.[0088] In accordance with the provisions of the patent statutes, the principleand mode of operation of this invention have been explained and illustrated inits preferred embodiment. However, it must be understood that this inventionmay be practiced otherwise than as specifically explained and illustratedwithout departing from its spirit or scope.

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What is claimed is:1. A system for management of virus data, the system comprising:one or more graphical-user interface (GUI) tools, anda data-storage and retrieval system (DSRS), wherein the DSRS stores

genetic, biological, clinical and phenotypic virus data and the one or more GUItools operate to effect control of the system to manage and analyze the data,and wherein the one or more GUI tools and the DSRS are integrated for thefor management of the virus data without exporting data.

2. The system of claim 1, further comprising an annotation tool thatmanages annotations in the form of user defined data points and integratesthe annotations into a searchable context that is inherent to the system.

3. The system of claim 1, further comprising a relational databaseengine integrated with the DSRS.

4. The system of claim 1, further comprising an import tool thatautomates a task of separating individual proteins and regions of from virussequences.

5. The system of claim 1, wherein at least one of the GUI toolspresents nucleotide and amino acid views and is operable to toggle betweenthe views.

6. The system of claim 1, further comprising a query tool thatisolates user-defined genetic characteristics via sequence-associatedannotations.

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7. The system of claim 6, further comprising an alignment tool linkedto the query tool to enable one or more query attributes to be highlighted in analignment function.

8. The system of claim 7, wherein the alignment tool comprises acontig assembler that analyzes complete and partial genomic sequences

9. The system of claim 1, further comprising a phylogeny tool thatassembles alignments into evolutionary trees that color-code and time-stampdata sequences.

10. The system of claim 1, further comprising a graphics tool thatpresents raw electropherogram data and assembles at least one of a linegraph or a bar graph to plot variables and presents these graphics.

11. The system of claim 1, further comprising a query tool that linksrelational virus data sets.

12. The system of claim 1, further comprising a query tool that selectsvirus sequences via user-defined attributes from a list of annotations pre-associated with the sequences.

13. The system of claim 12, wherein the query tool comprisesannotations and operators which are user selected and set to control queryresults.

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14. The system of claim 1, further comprising an alignment tool, aphylogenetics tool and a mutation analysis tool, wherein the alignment,phylogenetics and mutation analysis tools are integrated in one place.

15. The system of claim 14, wherein the alignment, phylogeneticsand mutation analysis tools are specifically tailored to mathematics of virusreplication rate and error-prone polymerase.

16. The system of claim 1, comprising an architecture comprised ofthree tiers, comprising a presentation tier, a middleware tier and a databasetier with interaction object layers, wherein the presentation tier comprises oneor more GUI components including the one or more GUI tools, the middlewaretier comprises one or more middleware components and houses processinglogic used by the system, and the database tier comprises one or more datacomponents including the data-storage and retrieval system.

17. The system of claim 16, wherein at least one of the one or moreGUI tools comprises one or more windows forms served to a user from thepresentation tier, the one or more windows forms taking input from the userand displaying output, and wherein the processing logic processes the inputand returns the output to the one or more windows forms.

18. The system of claim 1, further comprising at least one toolselected from at least one of a group of an annotation tool, an alignment tool,a contig assembler, a phylogenetics tool, a mutation analysis tool, a graphicstools, a query tool, mutation tracking tool, an entropy tool, microarray datahandling tool and a genotyping tool.

19. The system of claim 1, further comprising statistical routines.

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20. The system of claim 1, further comprising an N Tier structure thatallows for the system to be scaled across disparate hardware resourceswithout the need to retool.

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ABSTRACT OF THE DISCLOSUREA system and method for managing virus data may include software

tailored for rapid, efficient and flexible management of virus data. The systemmay easier overcome data management problems. Moreover, the systemmay streamline the serious bottleneck of data management, significantlycompressing time between data collection and cure discovery. The systemmay comprise graphical-user interface (GUI) tools and a data-storage andretrieval system. It may also include a commercial relational database engine.The system may include annotation, alignment, phylogenetics and mutationanalysis tools. The alignment tool may be linked to a query tool and include acontig assembler. The system may include mutation tracking, reportgeneration and entropy measurement tools, as well as statistical routines andsecurity and installation packages. The system may include a softwarearchitecture comprised of three tiers: a presentation (GUI) tier, a middleware(Domain) tier, and a relational database management system (RDBMS) tier.

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PTO/SB/01 (04-09)Approved for use through 06/30/2010. OMB 0651-0032

U.S. Patent and Trademark Off ice; U.S. DEPARTMENT OF COMMERCEUnder the Paperwork Reduction Ac t of 1995, no persons are required to respond to a collect ion of information unless it contains a valid OMB control number.

DECLARATION - Utility or Design Patent Application

Claim of Foreign Priority BenefitsI hereby claim foreign priority benefits under 35 U.s.C. 119(a)-(d) or (f), or 365(b) of any foreign application(s) for patent,inventor's or plant breeder's rights certificate(s), or 365(a) of any PCT international application which designated at least onecountry other than the United States of America, listed below and have also identified below, by checking the box, any foreignapplication for patent, inventor's or plant breeder's rights certificate(s), or any PCT international application having a filing datebefore that of the application on which priority is claimed.

Prior Foreign Application Country Foreign Fil ing Date Priority Certified Copy Attached?Number(s) (MM/DDIYYYY) Not Claimed YES NOD D DD D DD D DD D DD Additional foreign application number(s) are listed on a supplemental priori ty data sheet PTO/SB/02B attached hereto.

[Page 2 of 3]


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PTO/SB/01 (04-09)Approved for use through 06/30/2010. OMB 0651-0032

U.S. Patent and Trademark Off ice; U.S. DEPARTMENT OF COMMERCEUnder the Paperwork Reduction Ac t of 1995, no persons are required to respond to a collect ion of information unless it contains a valid OMB control number.

DECLARATION - Utility or Design Patent Application

The addressDirect all ~ associated with E 3422 I OR D Correspondencecorrespondence to: Customer Number: address belowNameAddress

City State Zip

Country Telephone Email

WARNING:Petitioner/applicant is cautioned to avoid submitting personal information in documents filed in a patent application that maycontribute to identity theft. Personal information such as social security numbers, bank account numbers, or credi t card numbers(other than a check or credit card authorization form PTO-2038 submitted for payment purposes) is never required by theUSPTO to support a petition or an application. If this type of personal information is included in documents submitted to theUSPTO, petitioners/applicants should consider redacting such personal information from the documents before submitting themto the USPTO. Petitioner/applicant is advised that the record of a patent application is available to the public after publication ofthe application (unless a non-publication request in compliance with 37 CFR 1.213(a) is made in the application) or issuance ofa patent. Furthermore, the record from an abandoned application may also be available to the public if the application isreferenced in a published application or an issued patent (see 37 CFR 1.14). Checks and credit card authorization formsPTO-2038 submitted for payment purposes are not retained in the application file and therefore are not publicly available.Petitioner/applicant is advised that documents which form the record of a patent application (such as the PTO/SB/01) are placedinto the Privacy Act system of records DEPARTMENT OF COMMERCE, COMMERCE-PAT-7, System name: Patent ApplicationFiles. Documents not retained in an application file (such as the PTO-2038) are placed into the Privacy Act system ofCOMMERCE/PAT -TM-1 0, System name: Deposit Accounts and Electronic Funds Transfer Profiles.I hereby declare that all statements made herein of my own knowledge are true and that all statements made on information andbelief are believed to be true; and further that these statements were made with the knowledge that willful false statements andthe like so made are punishable by fine or imprisonment, or both, under 18 U.s.C. 1001 and that such willful false statementsmay jeopardize the validity of the application or any patent issued thereon.

NAME OF SOLE OR FIRST INVENTOR: l A petition has been filed for this unsigned inventorGiven Name (first and middle [if any]) Family Name or SurnameJohanna C. CraigInventor's Signature Date

Residence: City State Country CitizenshipNewport VA USA USAMailing Address180 Orchard Hill LaneCity State Zip CountryNewport VA 24128 USA~ Additional inventors or a legal representative are being named on the 1 supplemental sheet(s) PTO/SB/02A or 02LR attached hereto

[Page 3 of 3]


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Privacy Act StatementThe Privacy Act of 1974 (P.L. 93-579) requires that you be given certain information in connect ion withyour submission of the attached form related to a patent application or patent. Accordingly, pursuant tothe requirements of the Act, please be advised that: (1) the general authority for the collection of thisinformation is 35 U.S.C. 2(b)(2); (2) furnishing of the information solicited is voluntary; and (3) theprincipal purpose for which the information is used by the U.S. Patent and Trademark Office is to processand/or examine your submission related to a patent application or patent. If you do not furnish therequested information, the U.S. Patent and Trademark Office may not be able to process and/or examineyour submission, which may result in termination of proceedings or abandonment of the application orexpiration of the patent.The information provided by you in this form will be subject to the following routine uses:

1. The information on this form will be treated confidentially to the extent allowed under theFreedom of Information Act (5 U.S.C. 552) and the Privacy Act (5 U.S.C 552a). Recordsfrom this system of records may be disclosed to the Department of Justice to determinewhether disclosure of these records is required by the Freedom of Information Act.2. A record from this system of records may be disclosed, as a routine use, in the course ofpresent ing evidence to a court, magistrate, or administrative tribunal, including disclosuresto opposing counsel in the course of settlement negot iat ions.3. A record in this system of records may be disclosed, as a routine use, to a Member ofCongress submitting a request involving an individual, to whom the record pertains, whenthe individual has requested assistance from the Member with respect to the subject matterof the record.4. A record in this system of records may be disclosed, as a routine use, to a contractor of theAgency having need for the information in order to perform a contract. Recipients ofinformation shall be required to comply with the requirements of the Privacy Act of 1974, asamended, pursuant to 5 U.S.C. 552a(m).5. A record related to an International Application filed under the Patent Cooperation Treaty inthis system of records may be disclosed, as a routine use, to the International Bureau of theWorld Intellectual Property Organizat ion, pursuant to the Patent Cooperation Treaty.6. A record in this system of records may be disclosed, as a routine use, to another federalagency for purposes of National Security review (35 U.S.C. 181) and for review pursuant tothe Atomic Energy Act (42 U.S.C. 218(c)).7. A record from this system of records may be disclosed, as a routine use, to theAdministrator, General Services, or his/her designee, during an inspection of recordsconducted by GSA as part of that agency's responsibility to recommend improvements inrecords management practices and programs, under authority of 44 U.S.C. 2904 and 2906.Such disclosure shall be made in accordance with the GSA regulations governing inspectionof records for this purpose, and any other relevant (i.e., GSA or Commerce)directive. Such disclosure shall not be used to make determinations about individuals.8. A record from this system of records may be disclosed, as a routine use, to the public aftereither publication of the application pursuant to 35 U.S.C. 122(b) or issuance of a patentpursuant to 35 U.S.C. 151. Further, a record may be disclosed, subject to the limitations of37 CFR 1.14, as a routine use, to the public if the record was filed in an application whichbecame abandoned or in which the proceedings were terminated and which application isreferenced by either a published application, an application open to public inspection or anissued patent.

9. A record from this system of records may be disclosed, as a routine use, to a Federal,State, or local law enforcement agency, if the USPTO becomes aware of a violation orpotential violation of law or regulation.


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Under the Paperwork Reduct ion Act of 1995

PTO/SB/02A (07-07)Approved for use through 06/30 /2010. OMB 0651-0032U.S. Patent and Trademark Office; U.S. DEPARTMENT OF COMMERCE

no persons are required to respond to a collect ion of information unless it contains a valid OMB control number.ADDITIONAL INVENTOR(S) ]Supplemental Sheet Pace 1 of 1DECLARATION

Name of Additional Joint Inventor, if any: I D A petition has been filed for this unsigned inventorGiven Name (first and middle (if any)) Family Name or Surname

Jul ian H. Capps

Inventor'sSiqnature DateAus1in, TX USA USAResidence: City State Country Citizenship501 E. S1assney Lane 1433

Mailinq AddressAus1in TX 78745 USACity State Zip Country


Inventor'sSignature Date

Residence: City State Country Citizenship

Mailing Address

City State Zip Country


Inventor'sSignature Date

Residence: City State Country Citizenship

Mailing Address

City State Zip CountryThis col lection of information IS required by 35 U.S.C. 115 and 37 CFR 1.63. The informat ion IS required to obtain or retain a benefit by the public which IS to file(and by the USPTO to process) an application. Confidentiality is governed by 35 U.S.C. 122 and 37 CFR 1.11 and 1.14. This collection is estimated to take 21minutes to complete, inc luding gathering, preparing, and submit ting the completed application form to the USPTO. Time will vary depending upon the individualcase. Any comments on the amount of time you require to complete this form and/or suggest ions for reducing this burden, should be sent to the Chief InformationOfficer, U.S. Patent and Trademark Office, U.S. Department of Commerce, P.O. Box 1450, Alexandria, VA 22313-1450. DO NOT SEND FEES OR COMPLETEDFORMS TO THIS ADDRESS. SEND TO: Commissioner for Patents, P.O. Box 1450, Alexandria, VA 22313-1450.

If you need assistance in complet ing the form, caI /1-800-PTO-9199 (1-800-786-9199) and select option 2.


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PTO/SB/02B (07-07)Approved for use through 06/30 /2010. OMB 0651-0032

U.S. Patent and Trademark Office; U.S. DEPARTMENT OF COMMERCE. . . . . .

DECLARATION - Supplemental Priority Data SheetForeign applications:

Prior Foreign Application Foreign Filing Date Priority Certified Copy Attached?Number(s) Country (MM/DDIYYYY) Not Claimed YES NOD D D

D D DD D DD D DD D DD D DD D DD D DD D DD D DD D DD D DD D DD D DD D DD D DD D DD D D

This col lection of information IS required by 35 U.S.C. 115 and 37 CFR 1.63. The information IS required to obtain or retain a benef it by the public which IS to file(and by the USPTO to process) an application. Confidentiality is governed by 35 U.S.C. 122 and 37 CFR 1.11 and 1.14. This collection is estimated to take 21minutes to complete, including gathering, preparing, and submit ting the completed applicat ion form to the USPTO. Time will vary depending upon the individualcase. Any comments on the amount of time you require to complete this form and/or suggestions for reduc ing this burden, should be sent to the Chief InformationOfficer, U.S. Patent and Trademark Office, U.S. Department of Commerce, P.O. Box 1450, Alexandria, VA 22313-1450. DO NOT SEND FEES OR COMPLETEDFORMS TO THIS ADDRESS. SEND TO: Commissioner for Patents, P.O. Box 1450, Alexandria, VA 22313-1450.

If you need assistance in complet ing the form, caI /1-800-PTO-9199 (1-800-786-9199) and select option 2.


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Privacy Act StatementThe Privacy Act of 1974 (P.L. 93-579) requires that you be given certain information in connectionwith your submission of the attached form related to a patent application or patent. Accordingly,pursuant to the requirements of the Act, please be advised that: (1) the general authority for thecollection of this information is 35 U.S.C. 2(b)(2); (2) furnishing of the information solicited is voluntary;and (3) the principal purpose for which the information is used by the U.S. Patent and TrademarkOff ice is to process and/or examine your submission related to a patent applicat ion or patent. If you donot furnish the requested information, the U.S. Patent and Trademark Office may not be able toprocess and/or examine your submission, which may result in termination of proceedings orabandonment of the application or expiration of the patent.The information provided by you in this form will be subject to the following routine uses:

1. The information on this form will be treated conf identially to the extent allowed under theFreedom of Information Act (5 U.S.C. 552) and the Privacy Act (5 U.S.C 552a). Records fromthis system of records may be disclosed to the Department of Justice to determine whetherdisclosure of these records is required by the Freedom of Information Act.2. A record from this system of records may be disclosed, as a routine use, in the course ofpresenting evidence to a court, magistrate, or administrative tribunal, including disclosures toopposing counsel in the course of settlement negotiations.3. A record in this system of records may be disclosed, as a routine use, to a Member ofCongress submitt ing a request involving an individual, to whom the record pertains, when theindividual has requested assistance from the Member with respect to the subject matter of therecord.4. A record in this system of records may be disclosed, as a routine use, to a contractor of theAgency having need for the information in order to perform a contract. Recipients ofinformation shall be required to comply with the requirements of the Privacy Act of 1974, asamended, pursuant to 5 U.S.C. 552a(m).5. A record related to an International Application f iled under the Patent Cooperat ion Treaty inthis system of records may be disclosed, as a routine use, to the Internat ional Bureau of theWorld Intellectual Property Organization, pursuant to the Patent Cooperation Treaty.6. A record in this system of records may be disclosed, as a routine use, to another federalagency for purposes of National Security review (35 U.S.C. 181) and for review pursuant tothe Atomic Energy Act (42 U.S.C. 218(c.7. A record from this system of records may be disclosed, as a routine use, to the Administrator,General Services, or his/her designee, during an inspection of records conducted by GSA aspart of that agency's responsibility to recommend improvements in records managementpractices and programs, under authority of 44 U.S.C. 2904 and 2906. Such disclosure shallbe made in accordance with the GSA regulations governing inspection of records for thispurpose, and any other relevant (i.e., GSA or Commerce) directive. Such disclosure shall notbe used to make determinations about individuals.8. A record from this system of records may be disclosed, as a routine use, to the public aftereither publication of the application pursuant to 35 U.S.C. 122(b) or issuance of a patentpursuant to 35 U.S.C. 151. Further, a record may be disclosed, subject to the limitat ions of 37CFR 1.14, as a rout ine use, to the public if the record was filed in an application whichbecame abandoned or in which the proceedings were terminated and which application isreferenced by either a published application, an application open to public inspection or anissued patent.9. A record from this system of records may be disclosed, as a routine use, to a Federal, State,or local law enforcement agency, if the USPTO becomes aware of a violation or potentialviolation of law or regulation.

Sample Non-Provisional Patent Application

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Transcript of Sample Non-Provisional Patent Application