An interactive genome browsing analysis and visualization method and system

Abstract

The present invention proposes an interactive genome browsing analysis and visualization method and system, which automates the bioinformatics analysis steps, constructs a database and compares sequencing data, and interactively compares and browses the genome. It can provide a new database for genome sequencing data retrieval and comparison based on the sequencing data input by the user, and links multiple analysis functions to perform customized bioinformatics analysis and obtain accurate analysis results.

Description

Technical Field

[0001] The present invention belongs to the field of gene sequencing and visualization technology, and in particular relates to an interactive genome browsing analysis and visualization method and system. Background Art

[0002] The statements in this section merely provide background information related to the present invention and do not necessarily constitute prior art.

[0003] Among numerous biological analysis websites, due to researchers' demand for simple operations, there is a very high demand and requirement for browsing and visualization technology of genome, transcriptome, proteome and other information.

[0004] For vertebrates, such as humans, there are still deficiencies in the websites that support the comparison and analysis of the genomes of such organisms. In particular, websites that include interactive functions and sufficient visualization are even scarcer, which cannot meet the analysis needs of the rapidly developing sequencing data of vertebrates.

[0005] Furthermore, they often lack comprehensive coverage, focusing solely on a single aspect of database or function analysis, failing to consider or connect multiple aspects. They also lack simultaneous analysis coverage for multiple species, preventing timely interactive visualization, and lacking user-friendliness in configuration options. Summary of the Invention

[0006] To overcome the deficiencies of the above-mentioned prior art, the present invention provides an interactive genome browsing, analysis, and visualization method and system. Based on the sequencing data input by the user, a new database is provided for genome sequencing data retrieval and comparison. Furthermore, the system links analysis functions from multiple aspects to perform customized bioinformatics analysis and obtain accurate analysis results.

[0007] To achieve the above objectives, one or more embodiments of the present invention provide the following technical solutions:

[0008] According to a first aspect of an embodiment of the present invention, an interactive genome browsing, analysis, and visualization method is provided, comprising:

[0009] Collecting genome and gene locus association information data of organisms, and using the data to build an association database and store the above data;

[0010] Constructing a user interaction interface and obtaining the associated data of the genome and gene loci of the organisms in the database;

[0011] Visualize and interactively analyze the genome and gene locus association data of organisms using a whole-genome browser;

[0012] Based on the organism selected by the user, the associations and raw data of the analyzed and processed sequencing data are presented, enabling user-defined complete downloads.

[0013] According to another aspect of an embodiment of the present invention, an interactive genome browsing, analysis, and visualization system is provided, comprising:

[0014] A data collection unit, used to collect genome and gene locus association information data of organisms;

[0015] A database unit, used for constructing an association database based on the association and information of the genome and gene sites of the organism;

[0016] Interaction unit, used to provide a user interaction interface through Web front-end technology;

[0017] The basic information unit is used to obtain information about the genomes and gene loci of two organisms and to obtain the association between the genomes and gene loci of two organisms.

[0018] It also includes: a genome collinearity analysis unit, which is used to obtain the association between biological genome sequencing data and their relationships, perform visual and interactive whole genome browser analysis, and specifically implement the search, comparison and analysis of gene sequencing data.

[0019] The genome browser unit is used to perform biological browser functions, genome browser functions, and sequence browser functions, forming a comprehensive analysis from large to small;

[0020] The download unit is used to present the associations formed by the processed sequencing data and the original data according to the organism selected by the user, realizing a complete download function that can be customized by the user.

[0021] One or more of the above technical solutions have the following beneficial effects:

[0022] Based on the scheme, sequencing data of biological genomes with different numbers of genomes can be effectively processed; multiple interactive visualization functions are integrated and jointly analyzed, including a genome collinearity analysis unit, a gene collinearity analysis unit, a genome browser unit, and a download unit; at the same time, the scheme provides a user-friendly processing method, and users can interactively operate all functions on the website. Through simple selection, the tools can be freely configured in each processing step, and the visualization of the functions can be freely and interactively operated.

[0023] Advantages of additional aspects of the present invention will be given in part in the following description and in part will be obvious from the following description, or will be learned through practice of the present invention. BRIEF DESCRIPTION OF THE DRAWINGS

[0024] The accompanying drawings, which constitute a part of the present invention, are used to provide a further understanding of the present invention. The exemplary embodiments of the present invention and their descriptions are used to explain the present invention and do not constitute improper limitations on the present invention.

[0025] Figure 1 It is a functional module flow chart of the present invention;

[0026] Figure 2 It is the overall functional association diagram of the present invention; DETAILED DESCRIPTION

[0027] It should be noted that the following detailed descriptions are exemplary and intended to provide further explanation of the present invention. Unless otherwise specified, all technical and scientific terms used herein have the same meaning as commonly understood by those skilled in the art to which the present invention belongs.

[0028] It should be noted that the terms used herein are for describing particular embodiments only and are not intended to limit the exemplary embodiments according to the present invention.

[0029] In the absence of conflict, the embodiments of the present invention and the features thereof may be combined with each other.

[0030] The overall idea proposed by the present invention is: a user-friendly interactive genome browsing analysis and visualization method, which automates the bioinformatics analysis steps for researchers and clinicians without professional bioinformatics knowledge, including vertebrate database construction, sequencing data alignment, interactive genome comparison and browsing, and visualization technology. At the same time, it can provide a new database for genome sequencing data retrieval and alignment based on the sequencing data input by the user, and link multiple analysis functions to perform customized bioinformatics analysis, obtain accurate analysis results and provide users with download.

[0031] Example 1

[0032] This embodiment discloses an interactive genome browsing, analysis, and visualization method, comprising the following steps:

[0033] Step 1: Collecting the genome and gene locus association information data of the organism, and using the data to build an association database and store the above data;

[0034] Step 2: constructing a user interaction interface and obtaining the associated data of the genome and gene loci of the organisms in the database;

[0035] Step 3: Visualize and interactively analyze the genome and gene locus association data of the organism using a whole-genome browser;

[0036] Step 4: Based on the organism selected by the user, the associations formed by the analyzed and processed sequencing data and the original data are presented, enabling user-defined complete download.

[0037] In step one, the genome, gene and sequence information of relevant organisms are collected, the associations between genomes, genes and sequences between organisms are mined, and an association database is constructed.

[0038] like Figure 2 As shown, the species module collects genome, gene, and sequence information of related organisms, explores the associations between genomes, genes, and sequences, supports joint genome analysis of multiple organisms, and constructs a linked database. The linked database contains all the collected genetic information of the organisms, with each gene corresponding to the corresponding gene sequence. In addition, the linked database contains information on gene associations and sequence associations for the entire genome. Figure 2 The schema of the database is listed, which may contain thousands or tens of thousands or more different gene-related information for each organism.

[0039] The association database contains gene association information and sequence association information of the complete genome and lists the database architecture, which greatly reduces the threshold for user use. All data is saved through the website cloud database file to support the visualization of biological genome associations and interactive whole-genome and whole-gene comparison and viewing.

[0040] Provide open source code and open source data for users to modify and customize configuration.

[0041] In step 2, the user interaction interface is constructed and the associated data of the genome and gene loci of the organism in the database are obtained as follows:

[0042] Using Web front-end technology, we build a multi-layer canvas-style double-layer canvas interaction, synchronously display static images and implement animations and mouse actions on static images. We also use native JavaScript to respond to mouse action events. Based on different mouse actions, we can left-click to select the interactive biological genome information range, implement user-operable zoom operations, and right-click to select to view gene association information.

[0043] By using pre-processed databases, queries, and comparisons, we build associations between the genomes of organisms, and present these associations on web pages using web front-end technology, enabling interactive queries for users and providing more than one hundred organisms for users to select and query.

[0044] In step three, the association data of the genome and gene loci of the organism are visualized and analyzed interactively using a whole genome browser. Specifically,

[0045] Visualization and Interaction Methods: This allows for querying, searching, and basic pre-processing of information within the aforementioned database unit, providing it for the aforementioned browsing module and visualization functions. For example, in the Dot Plot function, based on the gene's position within the entire genome, the gene is plotted as a coordinate point, and the gene position is normalized to coordinates on the X and Y axes. Finally, the processed genome length, X and Y coordinates of the gene position, genome name, and the position of the genome axes are transmitted to the front-end. For information on how to present the information on the front-end, see the "Interaction Unit - Utilizing Web Front-end Technology" section.

[0046] The user inputs a sequence and provides a BLAST search. Based on the search results, the user is provided with the positions of similar sequences to the user input sequence on all chromosomes of the organism.

[0047] The Species Browser allows users to search for organisms based on their genome copy number and any keywords. The search includes the species' scientific name, common name, copy number, and taxonomic classification.

[0048] The implemented Genome Browser integrates with the Genome Broswer and extends its functionality based on its interface. Users can select the species, chromosome number, and the desired chromosome start and end positions to directly view the desired region. This feature is also integrated with other functions, allowing users to view genomes and genes on the entire chromosome at any time while viewing them in other functions.

[0049] The implemented Sequence Browser allows users to enter a gene name and search for related gene names and gene descriptions. An organism option allows users to select a specific organism to narrow the search. Furthermore, users can click dynamically generated links in the sequence search results to jump directly to several other related features on the website.

[0050] After completing the interactive data analysis and visualization, all open-source data used for website analysis is available for download. Based on the user's selected organism, the processed sequencing data is presented alongside the original data. Users can customize the download of complete genome sequences, genome annotation files, and associated information files.

[0051] Example 2

[0052] The present invention provides an interactive genome browsing, analysis and visualization system, comprising:

[0053] like Figure 1 As shown, the system includes the following multiple units, and the relationship between functions is indicated by arrows in each function.

[0054] The data collection unit is used to collect genome and gene locus association information for organisms. It collects genome, gene, and sequence information for related organisms, explores associations between genomes, genes, and sequences, supports joint genome analysis of multiple organisms, and constructs an association database. The association database contains all the collected genetic information for each organism, with each gene corresponding to a corresponding gene sequence. Furthermore, the association database contains information on gene associations and sequence associations for the entire genome. Figure 2 The schema of the database is listed, which may contain thousands or tens of thousands or more different gene-related information for each organism.

[0055] A database unit, used for constructing an association database based on the association and information of the genome and gene sites of the organism;

[0056] Interaction unit, used to provide a user interaction interface through Web front-end technology;

[0057] The basic information unit is used to obtain information about the genomes and gene loci of two organisms and to obtain the association between the genomes and gene loci of two organisms.

[0058] Also includes:

[0059] The genome collinearity analysis unit is used to obtain the association between biological genome sequencing data and their relationships, perform visual and interactive whole-genome browser analysis, and specifically implement the search, comparison and analysis of gene sequencing data.

[0060] The genome browser unit is used to perform biological browser functions, genome browser functions, and sequence browser functions, forming a comprehensive analysis from large to small;

[0061] The download unit is used to present the associations formed by the processed sequencing data and the original data according to the organism selected by the user, realizing a complete download function that can be customized by the user.

[0062] Furthermore, the user's usage threshold is greatly reduced, and all data is stored in the website's cloud database files; it is used to support the visualization of biological genome associations and interactive whole-genome and whole-gene comparison and viewing.

[0063] Provide open source code and open source data for users to modify and customize configuration.

[0064] Using pre-processed databases, queries, and comparisons, we build genomic associations between organisms. These associations are then presented on a web page using web front-end technology, enabling interactive user queries. We offer a large collection of over 100 organisms for users to select and query.

[0065] Furthermore, the database unit in the interactive genome browsing and analysis technology and visualization system specifically collects genome, gene, and sequence information of related organisms, explores the associations between genomes, genes, and sequences between organisms, supports joint genome analysis of multiple organisms, and constructs a correlation database. The correlation database contains all the collected genetic information of the organisms, with each gene corresponding to the corresponding gene sequence. Furthermore, the correlation database contains information on gene associations and sequence associations for the entire genome. Figure 2 The schema of the database is listed, which may contain thousands or tens of thousands or more different gene-related information for each organism.

[0066] The interaction units are:

[0067] Leveraging web front-end technology, a dual-layer canvas, similar to the multi-layer canvas of drawing software like Photoshop, is constructed to enable the simultaneous, integrated display of static images, animation, and mouse actions within these images. Native JavaScript is used to respond to mouse action events. Based on different mouse actions, left-click selection allows for interactive selection of biological genome information, user-operable zooming, and right-click selection allows for viewing gene-related information. This technology enables users to interactively view, search, and download gene sequences and related information.

[0068] The basic information unit specifically implements querying, searching, and basic information preprocessing of the information in the aforementioned database units, providing it to the aforementioned browsing module and visualization functions. For example, in the Dot Plot function, based on the gene's position in the entire genome, the gene is used as a coordinate point in the plot, and the gene position is normalized to coordinates on the X and Y axes. Finally, the processed genome length, the X and Y coordinates of the gene position, the genome name, the position of the genome axis, and other information are transmitted to the front end.

[0069] Furthermore, the genome collinearity analysis unit is specifically:

[0070] In the Dot Plot function implemented by this technology, the gene is used as a coordinate point in the graph based on its position in the whole genome, and the gene position is normalized to coordinates on the X-axis and Y-axis. Finally, the processed genome length, X, Y coordinates of the gene position, genome name, genome axis position and other information are transmitted to the front end.

[0071] The Circos Plot function implemented by this technology pre-processes images between species and stores them on the server to speed up website response, reduce user waiting time, enhance user experience, and achieve visual graphical analysis of gene associations between the whole genomes of two organisms in a circular graph.

[0072] Among them, including the use of gene collinearity analysis units, specifically,

[0073] In the Locus Search function implemented by this technology, users can enter a gene name to search for the relative position relationship between any two species collected on this website.

[0074] In the BLAST function implemented by this technology, users can input DNA or protein sequences. This technology provides a BLAST search for the input sequence and, based on the search results, provides the user with the locations of similar sequences to the input sequence on all chromosomes of the organism.

[0075] Furthermore, the genome browser unit is specifically:

[0076] The Species Browser, implemented using this technology, allows users to search for organisms based on their genome copy number and any keyword. This includes the species' scientific name, common name, copy number, and taxonomic classification.

[0077] The Genome Browser feature implemented by this technology integrates with Genome Broswer and expands its functionality based on its interface. Users can select the species, chromosome number, and the desired chromosome start and end positions to directly view the desired region. This feature is also integrated with other features, allowing users to view genome and gene status across the entire chromosome at any time while viewing genomes and genes in other features.

[0078] The Sequence Browser feature implemented with this technology allows users to enter a gene name and search for related gene names and gene descriptions. It also includes an organism option that allows users to select a specific organism to narrow the search. Furthermore, users can click dynamically generated links in the sequence search results to directly jump to several other related features on the website.

[0079] Furthermore, the downloading unit is specifically:

[0080] This technology provides all open-source data used for website analysis for download. Based on the user's selected organism, the processed sequencing data is presented alongside the original data, enabling user-defined downloads of complete genome sequences, genome annotation files, and associated information files.

[0081] Example 3

[0082] The present invention provides a computer-readable instruction device, wherein when the computer instructions are executed by a processor, the interactive genome browsing analysis and visualization method is completed.

[0083] The following steps are performed:

[0084] Step 1: Collecting the genome and gene locus association information data of the organism, and using the data to build an association database and store the above data;

[0085] Step 2: constructing a user interaction interface and obtaining the associated data of the genome and gene loci of the organisms in the database;

[0086] Step 3: Visualize and interactively analyze the genome and gene locus association data of the organism using a whole-genome browser;

[0087] Step 4: Based on the organism selected by the user, the associations formed by the analyzed and processed sequencing data and the original data are presented, enabling user-defined complete download.

[0088] Example 4

[0089] The present invention provides a computer storage medium for storing and executing any one of the steps of the interactive genome browsing, analysis, and visualization method, specifically comprising:

[0090] Step 1: Collecting the genome and gene locus association information data of the organism, and using the data to build an association database and store the above data;

[0091] Step 2: constructing a user interaction interface and obtaining the associated data of the genome and gene loci of the organisms in the database;

[0092] Step 3: Visualize and interactively analyze the genome and gene locus association data of the organism using a whole-genome browser;

[0093] Step 4: Based on the organism selected by the user, the associations formed by the analyzed and processed sequencing data and the original data are presented, enabling user-defined complete download.

[0094] The steps involved in the apparatuses of Examples 2, 3, and 4 above correspond to those of Method Example 1. For detailed implementations, please refer to the relevant description of Example 1. The term "computer-readable storage medium" should be understood to mean a single medium or multiple media containing one or more instruction sets; it should also be understood to include any medium capable of storing, encoding, or carrying an instruction set for execution by a processor and causing the processor to perform any method of the present invention.

[0095] Those skilled in the art will appreciate that the modules or steps of the present invention described above can be implemented using a general-purpose computer device. Alternatively, they can be implemented using program code executable by a computing device, which can then be stored in a storage device and executed by the computing device. Alternatively, they can be fabricated into separate integrated circuit modules, or multiple modules or steps can be fabricated into a single integrated circuit module for implementation. The present invention is not limited to any specific combination of hardware and software.

[0096] Although the above describes the specific embodiments of the present invention in conjunction with the accompanying drawings, it is not intended to limit the scope of protection of the present invention. Those skilled in the art should understand that various modifications or variations that can be made by those skilled in the art on the basis of the technical solution of the present invention without any creative work are still within the scope of protection of the present invention.

Claims

1. An interactive genome browsing analysis and visualization method, characterized in that: The following steps are involved: Collecting genome and gene locus association information data of organisms, and using the data to build an association database and store the above data, specifically: collecting genome, gene and sequence information of related organisms, mining the association between genomes, genes and sequences of organisms, and building an association database; Constructing a user interaction interface and obtaining the associated data of the genome and gene loci of the organisms in the database; Visualize and interactively analyze the genome and gene locus association data of organisms using a whole-genome browser; Based on the organism selected by the user, the associations and raw data of the analyzed and processed sequencing data are presented, enabling user-defined complete downloads.

2. The interactive genome browsing analysis and visualization method according to claim 1, characterized in that: The association database contains complete genome-wide gene association information and sequence association information and lists the database architecture.

3. The interactive genome browsing analysis and visualization method according to claim 1, characterized in that: Using Web front-end technology, we build a multi-layer canvas-style double-layer canvas interaction, synchronously display static images and implement animations and mouse actions on static images. We also use native JavaScript to respond to mouse action events. Based on different mouse actions, we can left-click to select the interactive biological genome information range, implement user-operable zoom operations, and right-click to select to view gene association information.

4. The interactive genome browsing analysis and visualization method according to claim 1, wherein: The association data of the genome and gene loci of organisms are visualized and analyzed in an interactive whole-genome browser. Specifically, according to the position of the gene in the whole genome, the gene is used as a coordinate point in the graph, the position of the gene is normalized to the coordinates on the X-axis and Y-axis, and finally the processed genome length, X, Y coordinates of the gene position, genome name, and genome axis position information are transmitted to the front end.

5. The interactive genome browsing analysis and visualization method according to claim 4, characterized in that: The user inputs a sequence and provides a BLAST search. Based on the search results, the user is provided with the positions of similar sequences to the user input sequence on all chromosomes of the organism.

6. An interactive genome browsing analysis and visualization system, characterized in that: include: The data collection unit is used to collect the genome and gene site related information data of the organism, specifically: collecting the genome, gene and sequence information of the relevant organism; The database unit is used to construct an association database based on the association and information of the genome and gene sites of organisms, specifically: mining the association between the genomes, genes and sequences of organisms to construct an association database; Interaction unit, used to provide a user interaction interface through Web front-end technology; The basic information unit is used to obtain information about the genomes and gene loci of two organisms and to obtain the association between the genomes and gene loci of two organisms.

7. The interactive genome browsing analysis and visualization system according to claim 6, characterized in that: Also includes: The genome collinearity analysis unit is used to obtain the association between biological genome sequencing data and their relationships, conduct visual and interactive whole-genome browser analysis, and specifically implement the search, comparison and analysis of gene sequencing data; The genome browser unit is used to perform biological browser functions, genome browser functions, and sequence browser functions, forming a comprehensive analysis from large to small; The download unit is used to present the associations formed by the processed sequencing data and the original data according to the organism selected by the user, realizing a complete download function that can be customized by the user.

8. A computer-readable instruction device, characterized in that When the computer instructions are executed by a processor, the method according to any one of claims 1 to 5 is performed.

9. A computer storage medium, characterized in that Storing the method according to any one of claims 1 to 5.

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