Genome display and analysis system

Abstract

The invention discloses a genome display and analysis system which comprises a genome information and literature information acquisition module, a gene display module, a gene comparison module, a primer design module and a database established according to the method. The method has the characteristics that similar homologous genes among different species can be quickly obtained, genes or protein sequences among different species can be more accurately and quickly compared and analyzed, the genes can be quickly visualized in genomes, verified gRNA sequences can be displayed, tools can be integrally used, and time and labor can be saved.

Description

TECHNICAL FIELD

[0001] The present application relates to the technical field of bio-information analysis, and discloses a genome display and analysis system and a method for analyzing genes and genomes between species. BACKGROUND

[0002] With the continuous progress of sequencing technology, the sequencing quality is significantly improved, the read length is steadily increased, and the sequencing cost is continuously reduced, which enables more and more whole genome information of biological species or samples to be obtained more efficiently and economically, providing more valuable research resources for scholars.

[0003] The acquisition of whole genome information digitizes complex biological organisms, so that biological research can no longer rely only on traditional wet experimental approaches, but can also be carried out through dry experiments, i.e., using computers to deeply mine the whole genome information. The existence of whole genome information can help understand the biological organism from the source of life, i.e., genetic material, and provide a direction mark for biological research. These information can serve as a guide for experimental design and execution. However, to fully utilize the whole genome information, it is necessary to have a deep understanding of the genome information, and genome annotation is the first key step for understanding the genome information. The core task of genome annotation is to identify genes, and this process is completed by gene prediction software, which usually includes three methods of homology-based, model-based and de novo prediction. When the research species have close genetic relationship with other species that have been annotated, homologous gene prediction can be performed; when there is no such species, a statistical model can be learned from a large number of known gene sequences to identify the coding sequence and other components of the genome of the species to be studied; and in the case of not relying on known genes or proteins, potential coding regions can be directly identified from the genome sequence, i.e., de novo prediction.

[0004] For biological species that have been annotated but less studied, the whole genome data of different species can be downloaded to compare with similar species that have been studied more. The purpose of the present application is to provide a gene display and analysis system to directly display the similar homologous genes between the species to be studied and the species that have been studied, and to display the position information of the genes in the species to be studied, while linking to the known homologous genes for details. SUMMARY

[0005] Based on the above purpose, the present application first provides a genome display and analysis system, which comprises the following modules: (1) a genome information and literature information acquisition module of a target species, which is used to download the genome data, gene annotation data and progress information of the target species from network resources; (2) a gene display module for the target species, which is used to display the target species at the chromosome level, including gene browser, gene information display and gRNA information display; (3) a gene comparison module for the target species, which is used to realize the screening and analysis of similar genes in the genome of the target species and the genome of a comparative species, and the BLAST tool of NCBI is integrated into the gene comparison module as a localized BLAST module, with an expectation threshold of 0.01 and a display number of alignment results of 10; (4) a primer design module, which is based on a Web-based architecture, integrates the Primer3 program in the backend, accesses the primer design tool through the Internet, is used to perform actual primer design, and displays the parameters of the designed primer, including primer sequence, primer length, melting temperature, GC content, and gives a score according to each parameter of the primer.

[0006] In a preferred embodiment, in the genome acquisition module, the target species research progress information acquisition is to search from PubMed with biological Latin genus name, strain name and genome as keywords, and to periodically capture the latest published literature (for example, the top 15 articles) through scripts; and, the genome information is to search RefSeq reference genome data from NCBI with biological Latin genus name and strain name, download genome data, CDS sequence of genes to determine the number and length of genes, download gene annotation gtf, gff file to obtain functional annotation of genes, classify genes with specific protein name, functional description or protein sequence information as genes with protein annotation, classify genes without exact protein annotation information in the database, including genes annotated as pseudogenes, suspected proteins or hypothetical proteins, as genes without protein annotation; and, remove duplicate data, correct incorrect annotation information, exclude gene data with unclear or incomplete annotation information (integrity refers to including gene name, gene function, sequence characteristics, etc. being fully annotated. Genes lacking detailed annotation or having a large number of unknown functions are considered to have unclear, incomplete or low-quality annotation information), and use genome data visualization plug-ins to read and integrate genome data in the annotation file.

[0007] In a more preferred embodiment, the method of using genome data visualization plug-ins to read and integrate genome data in the annotation file is: Firstly, the genomic data stored in the annotation files in different formats is read by the genomic data visualization plug-in; then, the read genomic data is uniformly formatted and integrated by a data processing module in the genomic data visualization plug-in; wherein the data processing module includes a data format conversion function to convert the genomic annotation files in different formats into a uniform format for further processing and analysis of the data; and includes data cleaning of the integrated genomic data, including removing duplicates, correcting erroneous annotations and filling in missing data, etc., wherein the integrated genomic data also includes comparing and merging data from different sources to form genomic annotation information, wherein the data integration function of the data visualization plug-in can integrate genomic data from different species, different experimental conditions or different studies to provide cross-species or cross-condition genomic information.

[0008] In another preferred embodiment, in the gene display module, the gene browser displays the location of the gene on the genome; the gene information display part displays the GeneID on NCBI, the gene identifier, the gene function annotation, the corresponding protein accession number on NCBI, the description information of the corresponding protein, the scaffold number, the start and end site, the direction, the length, the DNA sequence, and the amino acid sequence.

[0009] In yet another preferred embodiment, in the gene comparison module, a JavaScript function is used to send an asynchronous request to the server for BLAST search, the server side queries the sequence for BLAST search, and returns the result to the client, finally, the returned result of the server is parsed and visualized in the webpage result area.

[0010] In a more preferred embodiment, the BLAST module in the gene comparison module includes blastn, blastp, blastx, tblastn, and tblastx, wherein the alignment word length size, score matrix, and gap penalty are set as follows: for the blastn program, the default word length is 11, the matching and mismatch scores are 2 and -3, and the gap penalty is Existence 5 and Extension 2; for the blastp, blastx, and tblastn programs, the default word length is 6, the score matrix is BLOSUM62, and the gap penalty is Existence 11 and Extension 1; and for the tblastx program, the default word length is 3, and the score matrix is BLOSUM62.

[0011] More preferably, the BLAST is downloaded from the NCBI website and the NCBI BLAST+ software package is installed, which includes command-line tools for locally performing BLAST; a local database is built using the makeblastdb tool to convert the biological database of interest into a format that can be searched by BLAST; a script or tool is written using the Python or Bash scripting language, which takes the provided sequence as input and calls the blastn, blastp, blastx, tblastn, or tblastx command; the output file of BLAST is parsed using the script or tool to extract the target information to be obtained, including the matching sequence, matching degree, and e-value; and the parsed results are presented in the form of a table or a graph.

[0012] In a preferred embodiment, in the gene comparison module, a program is written using the Golang development language to call the BLAST tool for sequence alignment and search, and the program is connected to the genome database system to communicate with the database and use the BLAST tool to compare and search sequences.

[0013] In another preferred embodiment, the target species is Pichia pastoris GS115, and the species to be compared is Saccharomyces cerevisiae S288C.

[0014] Secondly, the application provides a method for gene analysis using the above-mentioned target species genome display and analysis system, which comprises the following steps: (1) Genome information and literature information acquisition: downloading genome data, gene annotation data, and the latest information on genome research of the target species from network resources; (2) Gene display: visualizing and displaying the target species at the chromosome level, including a gene browser and gene information display; (3) Gene comparison: screening and analyzing similar genes in the genome of the target species and the species to be compared, wherein the gene comparison module integrates the BLAST tool of NCBI into a localized BLAST module, the expected threshold is 0.01, and the number of alignment results displayed is 10; (4) Primer design: the primer design module is based on a Web architecture, and the Primer3 program is integrated in the back end; the primer design tool is accessed through the Internet to perform actual primer design, and primer sequence, primer length, melting temperature, GC content, and scores according to each parameter of the primer are displayed.

[0015] In a preferred embodiment, the target species is Pichia pastoris GS115.

[0016] In a more preferred embodiment, the species to be compared is Saccharomyces cerevisiae S288C.

[0017] The present application integrates various tools, including gene, protein sequence alignment tools between different species, primer design tools required for gene verification. These tools or functions can be achieved in one key operation in the present application, greatly improving the efficiency of scientific research. Through the method of the present application, researchers can obtain the homologous genes of the concerned genes in the species to be compared and the functions of the genes by one-time search, and perform a series of alignment, primer design and other operations on the genes, thereby providing more comprehensive genomic information and more convenient and effective tools for researchers to better understand the species to be studied.

[0018] Compared with the prior art, the technical scheme of the present application has the characteristics of quickly obtaining similar homologous genes between different species, achieving more accurate and rapid comparative analysis of gene or protein sequence comparison between different species, realizing rapid visualization of genes in the genome, integrating the use of various tools, saving time and effort. In a specific embodiment of the present application, Pichia pastoris / Pichia formosana form yeast Komagataella phaffii As the target species, the present application solves the problem that there is no database for detailed analysis and annotation of the genome of Pichia pastoris engineering strain. After collecting and broadcasting the front-line literature related to Pichia pastoris, the genomic information, gene annotation information and phenotype data set of the example strain GS115 are integrated and structured, Saccharomyces cerevisiae is used as the species to be compared, and the gene information of Saccharomyces cerevisiae (taking the model strain S288C as an example) is compared with Pichia pastoris (taking the engineering strain GS115 as an example). The similar genes in the genomes of the two are visualized and displayed, one-key BLAST of the genes, proteins, etc. between Saccharomyces cerevisiae S288C and Pichia pastoris / Pichia formosana form yeast GS115 is realized, the results of the comparison between the two are quickly obtained, the efficiency of information search and acquisition is improved, and online primer design is also provided, which is versatile.

[0019] The technical scheme of the present application localizes the BLAST and NCBI Genome Viewer tools, integrates the use of various tools to quickly visualize the location information of the genes of the target species (for example, Pichia pastoris engineering strain GS115) in the genome, and realizes the function of rapid BLAST, which saves time and effort. BRIEF DESCRIPTION OF DRAWINGS

[0020] Figure 1 The figure is the overall flowchart of the inter-species gene and genome analysis method of the present application; Figure 2 The figure is the flowchart of the built-in similar homologous gene search method between different species; Figure 3 To display the gene list page of the present application, including gene screening options and gene overview information display; Figure 4 To display the gene detail page of the present application for specific genes; Figure 5 The result of the gene information part of the gene detail page presented after searching for the Pichia pastoris gene PAS_chr1-4_0614 (GeneID: 8197822) in the present application; Figure 6 is the alignment result of similar genes in Saccharomyces cerevisiae presented after blastp of the Pichia pastoris gene PAS_chr1-4_0614 in the present application; Figure 7 is the result of similar genes in Saccharomyces cerevisiae presented after blastp of the gene PAS_chr1-4_0614 in SGD; Figure 8 The YLR147C in the present application Figure 4 directly jumps to the detail page of the gene in SGD; Figure 9 is the one-key BLAST automatic filling page in the database of the present application. DETAILED DESCRIPTION

[0021] The advantages and characteristics of the present application will become more apparent with the description. However, these examples are only exemplary and do not constitute any limitation on the protection scope defined by the claims of the present application.

[0022] Figure 1 A method flowchart for inter-species gene and genome analysis by the genome display, comparison and analysis system provided by the present application is given, and the specific implementation scheme for constructing the genome display, comparison and analysis system described in the present application, as well as specific application examples, are introduced below.

[0023] Construction Example. Take Pichia pastoris / Pichia formosana strain GS115 as an example to construct the genome display and analysis system Those skilled in the art can understand that other species of strain genome display and analysis systems can also be constructed by applying the method provided by the present application. The present application provides a specific construction method for Pichia pastoris / Pichia formosana strain GS115 genome display and analysis system, which comprises: 1. Construction of genome information acquisition module The genome information described in the present application includes papers and documents related to genome information and genome composition information (1) Document information acquisition Target strains, such as GS115, related latest literature acquisition and display: from PubMed with Pichiapastoris, Komagataella phaffii, GS115, genome as keywords, find the latest published literature, and extract the literature name and the key figure in the literature on the home page for carousel display. The specific implementation is as follows: From PubMed, search for literature with Latin classification name, strain name and genome as keywords. Take GS115 as an example: Pichia pastoris, Komagataella phaffii, GS115, genome, etc. as keywords to find literature, get 808 pieces of literature, and extract the title of 15 latest published literature, the key figure and the abstract part in the literature on the home page for carousel display. Daily literature information is obtained and stored in the database through a script to realize data updating, which is obtained through Python crawler and stored in the local database.

[0024] (2) Genome data and gene annotation data acquisition: download the assembled reference genome data and gene annotation data from NCBI; Take GS115 as an example, search from NCBI to get 1 piece of RefSeq reference genome data of Komagataella phaffii strain GS115, 5040 pieces of gene data, download gene annotation gtf, gff file to obtain gene function annotation, and classify the genes with exact protein annotation information, including but not limited to specific protein name, function description or protein sequence information, as genes with protein annotation. The genes without exact protein annotation information in the database, including the genes annotated as pseudogenes, suspected proteins or hypothetical proteins, are classified as genes without protein annotation. Among them, 3432 genes have protein annotation data, and 1608 genes have no protein annotation data.

[0025] 2. Construction of gene display module The gene display module is a data visualization display of Pichia pastoris GS115 at the chromosome level, which includes gene browser and gene information display; according to the reference genome and gene annotation information of GS115, the number of genes on each chromosome, the number of genes with known functions, and the length of the whole chromosome are determined, and these information are displayed in the form of table and graph, wherein the number of genes and the number of annotated genes are set as hyperlinks to jump to the corresponding gene list page. The specific implementation is as follows: (1) Information determination 1) Determine the number and length of genes The number and length of genes can be determined according to the genome data and CDS sequence of genes downloaded from NCBI.

[0026] 2) Functional annotation of genes The functional annotation of genes can be obtained from the gene annotation gtf, gff files downloaded from NCBI.

[0027] (2) Integrating genomic data in annotation files The genomic data visualization (GDV) plugin is used to read and integrate genomic data in annotation files, which includes the following steps: first, use the GDV plugin to read the genomic data stored in different formats of annotation files; then, through the data processing module in the GDV plugin, the read genomic data is unified in format and integrated. The data processing module includes data format conversion function, which can convert different formats of genomic annotation files into a unified format, so as to facilitate further processing and analysis of data. Further including data cleaning of integrated genomic data, including removing duplicates, correcting wrong annotations and filling data missing, etc., to improve the quality and consistency of data.

[0028] The integrated genomic data also includes comparing and merging data from different sources to form more comprehensive and detailed genomic annotation information. The data integration function of the GDV plugin can be used to integrate genomic data from different species, different experimental conditions or different studies to support cross-species or cross-condition genomic research.

[0029] (3) Gene display The genomic assembly information obtained by the above steps is displayed on the web page in the form of tables and graphs using the react front-end framework. The following steps are used to achieve this: 1) Create a React application: First, create a new React application. You can use the command line tool (such as Create React App) or other ways to initialize a new React project.

[0030] 2) Component design: Design React components to display genomic assembly information. You can create multiple components, such as a table component and a graph component.

[0031] 3) Data transmission: Pass the genomic assembly information as data to the corresponding React components. This can be achieved by using the props attribute of React to pass data to child components. Ensure that the data structure matches the expected format of the component.

[0032] 4) Table display: In the table component, use React's built-in components (such as

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[0064] 、 、 and ) to create table structures. Based on the properties of the gene assembly information, loops are used to dynamically generate rows and columns of the table and fill data into the table. 5) Graphical presentation: In the graphical component, third-party graphics libraries (such as D3.js, Chart.js, etc.) are used to create charts. According to the characteristics of the gene assembly information, select the appropriate chart type to display the data. According to the different attributes of the data, convert it into the format required by the graphics library, and draw it into the graphics component. 6) Style and interaction: Add styles and interactive effects to the component to make the gene assembly information presented on the webpage in an intuitive and easy-to-understand way. Use CSS or CSS-in-JS libraries to add styles to the component, and use React's event handling mechanism to implement interactive functions such as mouseover effects or click to expand detailed information, etc. 7) Deployment and testing: After completing the development of the component, package the React application and deploy it to the web server. Make sure to test thoroughly before deployment to ensure compatibility and stability of the component on different browsers and devices. (4) Screening and analysis of similar genes The gene display and analysis system described in the present invention can screen and analyze similar genes based on the provided genes. The following shows the screening and analysis of similar genes in Pichia pastoris GS115 based on whether similar genes exist in Saccharomyces cerevisiae S288C, and gives a flowchart of the built-in method for searching for similar homologous genes between different species in the present invention. Take gene PAS_chr1-4_0614 as an example, get the nucleic acid sequence and protein sequence of the gene in the NCBI database https: / / www.ncbi.nlm.nih.gov / , through nucleic acid sequence or protein sequence BLAST comparison, protein sequence uses blastp program, comparison species and strain Saccharomyces cerevisiae S288C, expectation value 0.01, maximum display result number 10, word length 6, score matrix BLUSOM62, gap penalty Existence: 11, Extension: 1; nucleic acid sequence selects blasn program, comparison species and strain Saccharomyces cerevisiae S288C, expectation value 0.01, maximum display result number 10, word length 11, match score 2, mismatch score -3, gap penalty Existence: 5, Extension: 2. Find sequences from other species similar to the gene sequence or protein sequence, find gene sequences from Saccharomyces cerevisiae with high sequence identity and coverage, combine these sequences with the search gene PAS_chr1-4_0614 gene or protein sequence into a fasta file, use MAFFT for sequence alignment and trimming, and construct an evolutionary tree for phylogenetic analysis.The gene YLR147C in Saccharomyces cerevisiae, which is closest to the Pichia pastoris gene PAS_chr-4_0614 in terms of the closeness of the phylogenetic relationship, is the similar homologous gene of the gene in Saccharomyces cerevisiae. The standard name YLR147C and the systematic name SMD3 (indicating the gene function) of the Saccharomyces cerevisiae gene are searched in the database, and are recorded. The above operation is repeated to search for the similar homologous gene of the Saccharomyces cerevisiae gene in all genes of Pichia pastoris, and the similar genes are recorded and stored in the local storage. The gene list page is an overview of all genes, which are arranged in the order of gene identifiers by default, and can be classified and screened according to the chromosomal position of the gene, whether the function is annotated, and whether there is a similar gene in Saccharomyces cerevisiae S288C (analysis results presented from the association of similar genes in the gene comparison module), each gene displays the scaffold number, start and end site, direction, length, GeneID on NCBI, gene identifier, corresponding protein accession number on NCBI, and description information of the corresponding protein, and can be searched according to GeneID, gene identifier name or protein name, and directly jump to the detail page of the gene. The specific implementation is as follows: enter the list page, the page displays a total of 5040 data (as shown), the left filter bar filters the chromosomal position as "chromosome 1", and 1538 data are obtained, the gene type is further selected as "annotated protein gene", and 1056 data are obtained, and the similar gene to S288C is further selected, and 799 data are obtained. Taking GeneID 8197822 as an example, it can be displayed that it is located in chromosome 1, the scaffold number is NC_012963.1, the start site is 2554895, the end site is 2555197, the direction is "+", the gene identifier is PAS_chr1-4_0614, the protein access number is XP_002490753.1, the amino acid length is 100, and the protein annotation data is "Core Sm protein Sm D3" (as shown).The specific implementation is as follows: searching according to GeneID, gene identifier name or protein name, directly jumping to the detail page of the gene, taking the data of GeneID 8197822 as an example, the detail page data is divided into two parts of gene browser and gene information. The gene browser can directly display the position of the gene 8197822 on the GS115 genome. The gene information part displays the GeneID, gene identifier, corresponding protein accession number on NCBI, description information of the corresponding protein, scaffold number, start and end site, direction, length, DNA sequence, amino acid sequence and other data of the gene 8197822 on NCBI (as shown). The drop-down arrow on the right side of the gene information can select the required DNA, mRNA or protein amino acid sequence, and click the right side of the download to directly download one key. (6) The gene detail page is integrated with the gene browser, which can visually display the DNA, mRNA and amino acid of the gene in the genome. The Genome Viewer plug-in of NCBI is localized and displayed on the web page of the gene detail, which can directly display the position of the gene on the GS115 genome, and provide related information and link jump of the gene, mRNA and protein by mouse hovering. The specific implementation is as follows: taking the data of GeneID 8197822 as an example, the detail page data is divided into two parts of gene browser and gene information.Gene Browser can visually display the location of 8197822 gene on GS115 genome, and by mouse hovering over the gene band can provide: Gene: PAS_chr1-4_0614, Qualifiers: Partial start, Partial stop, Location: 2,554,895..2,555,197, Length: 303 nt, NC_012963.1 position 2,555,104, Gene position: 210; mouse hovering over the mRNA band can provide: mRNA: XM_002490708.1, Qualifiers: Partial start, Partial stop, Name: mRNA-Core Sm protein Sm D3, Location: 2,554,895..2,555,197, Span on NC_012963.1: 303 nt, Sequence length: 303 nt, NC_012963.1 position: 2,554,998, Exon: 1 of 1, CDS position: 104, mRNA position: 104, mRNA sequence: GCAAACTGGTTGAAT[C]TGAGGATTCCATGA; mouse hovering over the protein band can provide: CDS: XP_002490753.1, Name: Core Sm protein Sm D3, Location: 2,554,895..2,555,197, Span on NC_012963.1: 303 nt, Protein length: 100 aa, NC_012963.1 position: 2,555,048, Exon: 1 of 1, CDS position: 154, Protein position: 52, Protein sequence: DSMNIQLKDVTLTAQ[D]GKVSHEQIFIRGS, Download FASTA: XP_002490753.1, Ensembl Genomes-Gn: PAS_chr1-4_0614, Ensembl Genomes-Tr: CAY68473, Gene ID: 8197822 (PAS_chr1-4_0614), InterPro: IPR001163, IPR006649, IPR010920, IPR027141, UniProtKB / TrEMBL: C4QYZ9.In addition, the specific operation function pop-up window can be popped up by right-clicking the mouse on the bar, including: self-selected display interval, setting a new marker at the position, reversing the sequence chain, zooming in, zooming out, zooming in to the base sequence information, zooming in to the interval, setting the sequence start at the position, setting the sequence start point at the feature, etc. The DNA sequence and amino acid sequence display part of the gene detail page realizes one-key BLAST function, one-key jump to the locally integrated BLAST tool page, avoids sequence copy and paste, selection of different BLAST tools in different scenes and other operations, and facilitates rapid comparison with Saccharomyces cerevisiae S288C. The specific implementation method is as follows: taking the GeneID as 8197822 data as an example, click one-key BLAST beside the amino acid sequence data, one-key jump to the locally integrated BLAST tool page, directly search, quickly output the result, display 1 similar sequence with Saccharomyces cerevisiae S288C sequence, sequence ID YLR147C, and the difference between GS115 and S288C sequence can be directly displayed. 3. Construction of gene comparison module The gene comparison module integrates the BLAST tool of NCBI in the database. The functions of blastn, blastp, blastx, tblastn and tblastx of NCBI are displayed in the BLAST module, and the comparison between different strain genomes is carried out, for example, the comparison between S288C and GS115. BLAST default only displays the comparison species, strain, expected threshold value and maximum comparison result display number, and high-order algorithm parameters are not displayed by default. If adjustment is needed, the comparison word length size, score matrix, gap penalty and the like can be expanded to customize. The specific implementation method is as follows: (1) Similar gene correlation presentation For each gene or gene sequence or function in Pichia pastoris / Fawjiao form yeast GS115 genome, similarity search is carried out in Saccharomyces cerevisiae S288C, and through the link of each GS115 gene detail page in NCBI, jump to Japanese Kyoto Encyclopedia of Genes and Genomes / KEGG or Homologous Gene Database / OrthoDB database, and query similar genes. For each gene, the similar or homologous gene mapping table on KEGG / OrthoDB is grabbed and sorted, and the sorted table is read in the program and displayed on the gene list and gene detail page.The specific implementation is as follows: taking the gene PAS_chr1-4_0614 as an example, the nucleic acid sequence and protein sequence of the gene are obtained in the NCBI database https: / / www.ncbi.nlm.nih.gov / , by comparing the nucleic acid sequence or the protein sequence, the sequence similar to the gene sequence or the protein sequence derived from other species is found, the gene sequence from Saccharomyces cerevisiae with high sequence identity and coverage (the sequence identity and coverage vary according to the genetic relationship of different objects, and in general, the two values of the target species are the highest) is found, after combining these sequences with the gene or protein sequence of the searched gene PAS_chr1-4_0614 into a fasta file, the sequence alignment and trimming are performed, the phylogenetic tree is constructed by phylogenetic analysis. According to the genetic relationship shown in the phylogenetic tree, the gene YLR147C in Saccharomyces cerevisiae with the closest genetic relationship to the Pichia pastoris gene PAS_chr-4_0614 is the similar homologous gene of the gene in Saccharomyces cerevisiae. The standard name YLR147C and the systematic name SMD3 (indicating the function of the gene) of the Saccharomyces cerevisiae gene are searched in the database, and are recorded. Repeat the above operation to search for the similar homologous genes of all genes in Pichia pastoris in Saccharomyces cerevisiae, and record the similar genes. As shown, the "S288C similar gene" data can be selected in the left filter bar of the gene list page, a total of 3129, taking the GeneID as 8197822 data as an example, the S288C similar gene YLR147C is displayed in the gene information bar of the detail page. Clicking the S288C similar gene link can directly jump to the Saccharomyces cerevisiae genome database / SGD to view the details of the gene, as shown. (2) BLAST result detail page. The comparison result report first displays the comparison task, sequence length, comparison algorithm, and expectation threshold. The comparison result details include three blocks, which are comparison global overview, comparison result list, and comparison detail display. The global overview displays the names of the matched strains and the position information on the chromosome or scaffold, and is graphically displayed. The comparison result list displays the sequence information of the matched sequences, and the matched sequence length, various index score of the matching result are graphically presented. The comparison detail display displays the comparison of each amino acid or base of the specific comparison and matched sequence, and displays the specific values of the comparison, complete match, gap, comparison score, comparison mode, expectation, etc. The three blocks can be directly accessed by clicking the tab at the top of the detail page.The specific implementation is as follows: taking the blastp function as an example, in the present application, the amino acid sequence of the data with GeneID 8197822 is uploaded, compared with the Saccharomyces cerevisiae S288C strain, the expected threshold is selected as 0.01, the maximum number of comparison results is selected as 10, the algorithm parameters are selected as default values (the default word length is 6, the score matrix is BLOSUM62, the gap penalty Existence is 11 and the Extension is 1), the search is performed, the YLR147C XII sequence matched with S288C is obtained, the total score is 375.0, the sequence query coverage is 96.00%, the E value is 5.36819e-49, the maximum similarity rate is 68.75%, and the result is shown in FIG. 6 (,,). The same blastp is directly performed on the Saccharomyces cerevisiae genome database / SGD, and three search results are presented, three genes YLR147C, YER112W and YDR378C are searched, and only YLR147C is the most similar result to the Pichia pastoris search gene, and the search result is shown in FIG. 7 (,,,). The primer design module is integrated with a primer design tool, which can perform real-time online primer design for a certain gene. The specific implementation is as follows: taking the data with GeneID 8197822 as an example, the "Primer Design" module is selected for primer design. The system backend integrates the Primer3 program for performing actual primer design calculation. The primer design parameters can be customized according to experimental requirements, such as primer length, melting temperature range, GC content, etc. The target DNA sequence is input, and the system designs one or more pairs of primers based on the Primer3 algorithm. The primer information is displayed in a table form, including primer sequence, length, melting temperature, GC content and other key information, and a score is given according to the primer parameters. Clicking "Primer Design" beside the DNA sequence on the gene detail page will automatically import the DNA sequence of the data with GeneID 81978226 to the primer design page, the expected product size is selected as 100 bp-600 bp, 5 pairs of primer data are obtained, including the start site, length, product size, Tm value, GC content and sequence data of the primer.Application Example: Screening of Similar Genes in the Genomes of Saccharomyces cerevisiae S288C and Pichia pastoris / Komagataella phaffii GS115 1. Direct presentation of similar genes in the genomes of Saccharomyces cerevisiae S288C and Pichia pastoris / Komagataella phaffii GS115 is provided, and the details page of the similar gene in S288C in SGD can be accessed directly; taking the data with GeneID 8197822 as an example, the S288C similar gene YLR147C is displayed in the gene information column of the details page, and clicking can jump to the SGD database to view the details data of the gene (as shown); 2. One-key BLAST of genes, proteins, etc. between Saccharomyces cerevisiae S288C and Pichia pastoris / Komagataella phaffii GS115 is realized, and the results of the alignment between the two can be obtained quickly (as shown); taking the data with GeneID 8197822 as an example, click one-key BLAST next to the amino acid sequence data to jump to the locally integrated BLAST tool page for retrieval, and the results are directly output without waiting, showing that there is 1 similar sequence with Saccharomyces cerevisiae S288C sequence, and the sequence ID is YLR147C, which can directly display the differences between GS115 and S288C sequences. 3. BLAST and NCBI Genome Viewer tools are localized to quickly visualize the location information of GS115 genes on its genome and realize the function of fast BLAST. Taking the data with GeneID 8197822 as an example, click one-key BLAST next to the amino acid sequence data ( ), and jump to the locally integrated BLAST tool page for retrieval, see Figure 9 (, ), without waiting for the results to be directly output, showing that there is 1 similar sequence with Saccharomyces cerevisiae S288C sequence, and the sequence ID is YLR147C, which can directly display the differences between GS115 and S288C sequences, see Figure 6 (,, ). Comparative Example 1. Obtain the relevant frontier literature of GS115 Take PICHIA PASTORIS, KOMAGATAELLA PHAFFII, GS115, GENOME, etc. as keywords to search for literature in the PUBMED literature database. And carefully read and extract the key information, such as research purpose, method, result, etc. 2. Integrate and structure the data sets of the genome information and gene annotation information of Pichia pastoris / Komagataella phaffii (take GS115 as an example) First, download the genome sequence of GS115 and the annotation file of the genome sequence to the local computer to obtain the location and function of the gene. Use bioinformatics tools and software (such as BLAST, Bowtie, R, Python, etc.) to process these data. Finally, integrate these data sets into a unified format, structure the data by establishing a database or using table software, so as to facilitate subsequent analysis.3. Open the NCBI website and find the "BLAST" link on the homepage. Click on the BLAST page. In the BLAST page, select "nucleotide-nucleotide blast" or "protein-protein blast" according to the needs. Enter the GS115 sequence in the search box. If the sequence is in FASTA format, it can be directly pasted into the search box; if it is in other formats, it needs to be converted into FASTA format first. Set other parameters such as the selection of the database, the expected E-value threshold, etc. Click the "BLAST" button to start the comparison. Wait for the comparison result to return, which usually shows the most similar matching sequences and their related information to the user uploaded sequence. 4. Compare the gene information of Saccharomyces cerevisiae strain S288C with that of Pichia pastoris / Komagataella phaffii strain GS115 First, download the genome sequence and gene annotation information of S288C from public databases (such as NCBI, SGD, etc.). Then, use alignment tools (such as BLAST, ClustalW, etc.) to align the gene sequences of S288C with the genome sequences of GS115 to find similar genes between them. Output the alignment results to a format supported by a visualization tool (such as a BED file). Then, use a visualization tool (such as UCSC Genome Browser, Circos, etc.) to load the alignment results and set appropriate parameters (such as color, size, etc.) to display the location and relationship of the similar genes in the genome. Compared with the traditional BLAST method on the NCBI website BLAST page and SGD, the present application can quickly compare the sequences between the genes, proteins, and genes and proteins of Pichia pastoris GS115 and Saccharomyces cerevisiae S288C, which can lock the target gene faster and more accurately, improve the accuracy (such as the above example, which improves by 66.67%) and speed up the speed of getting the alignment results (such as the above example, which improves from 3.31s to 1.94s, accelerating by 41.39%).Compared with multiple steps of sequence alignment, screening, merging, phylogenetic tree construction, relationship searching and the like performed by using multiple databases and tools (the databases and tools that can be used include but are not limited to the NCBI database (https: / / www.ncbi.nlm.nih.gov / ), the KEGG database (https: / / www.genome.jp / kegg / ), the OrthoDB database (https: / / www.orthodb.org / ), the BLAST tool, the software MAFFT, MEGA, FastTree, IQTree, RAxML and the like), the Pichia pastoris GS115 gene can be quickly and accurately searched and positioned in the similar gene in Saccharomyces cerevisiae S288C, the similar homologous gene of the Pichia pastoris gene in Saccharomyces cerevisiae can be presented in one key mode, the search of homologous genes between different species is more convenient, and thus the work efficiency is improved. In the above embodiments, the description of each embodiment has different focuses, and the part not described in detail in a certain embodiment can be referred to the related description of other embodiments. It should be understood by those skilled in the art that the embodiments of the present application can be provided as a method, a system or a computer program product. Therefore, the present application can adopt a completely hardware embodiment, a completely software embodiment or an embodiment combining software and hardware aspects. Moreover, the present application can adopt a computer program product in the form of being implemented on one or more computer usable storage media (including but not limited to disk storage, CD-ROM, optical storage and the like) containing computer usable program codes. The above is only an embodiment of the present application and is not used to limit the present application. The present application can have various changes and modifications for those skilled in the art. Any modification, equivalent replacement, improvement and the like within the spirit and principle of the present application shall be included in the scope of claims of the present application.

Claims

1. A genomic display and analysis system, characterized by, The genome visualization and analysis system includes the following modules: (1) Target species genome information and literature information acquisition module, wherein the target species genome information and literature information acquisition module is used to download the target species reference genome data, gene annotation data and its research progress information from network resources; (2) A gene display module for the target species, wherein the gene display module for the target species is used for data visualization at the chromosome level, and the data visualization includes a gene browser, gene information display and gRNA information display; (3) Gene comparison module between target species and species to be compared, wherein the gene comparison module between target species and species to be compared is used to screen and analyze similar genes in the genome of target species and genome of species to be compared, wherein the gene comparison module integrates NCBI's BLAST tool into a localized BLAST module; (4) Primer design module. The primer design module is based on a Web architecture and integrates the Primer3 program in the backend. It accesses primer design tools through the Internet to perform actual primer design and displays the designed primer parameters, including primer sequence, primer length, melting temperature, GC content, and gives a score based on the primer parameters.

2. The genomic display and analysis system of claim 1, wherein, In the target species' genome information and literature information acquisition module, the literature information acquisition involves searching PubMed using keywords such as biological Latin species name, strain name, and genome, and periodically retrieving published literature within a set time period via a script; and... The genomic information was obtained by retrieving RefSeq reference genome data from NCBI using biological Latin species names and strain names, downloading genome data and gene CDS sequences to determine the number and length of genes, downloading gene annotation GTF and GFF files to obtain gene functional annotations, classifying genes with specific protein names, functional descriptions, or protein sequence information as protein-annotated genes, and classifying genes without specific protein annotation information in the database, including genes annotated as pseudogenes, speculative proteins, or hypothetical proteins, as unannotated protein genes. In addition, it removes duplicate data, corrects erroneous annotation information, excludes gene data with unclear or incomplete annotation information, and uses a genome data visualization plugin to read and integrate genome data in annotation files.

3. The genomic display and analysis system of claim 2, wherein, The method for using a genome data visualization plugin to read and integrate genome data from annotation files is as follows: First, a genome data visualization plugin is used to read genome data stored in annotation files of different formats. Then, the data processing module in the plugin performs format unification and data integration on the read genome data. This data processing module includes a data format conversion function to convert genome annotation files of different formats into a unified format for further data processing and analysis. It also includes data cleaning of the integrated genome data, including steps such as removing duplicates, correcting erroneous annotations, and filling in missing data. The integrated genome data also includes comparison and merging of data from different sources to form genome annotation information. The data integration function of the visualization plugin can integrate genome data from different species, experimental conditions, or studies, providing cross-species or cross-condition genomic information.

4. The genomic display and analysis system of claim 1, wherein, In the gene display module of the target species, the gene browser displays the location of the gene on the genome; the gene information display section displays the gene's NCBI GeneID, gene identifier, gene function annotation, corresponding protein accession number on NCBI, description information of the corresponding protein, scaffold number, start and stop sites, orientation, length, DNA sequence, and amino acid sequence; the gRNA information display section displays the location and orientation information of the gRNA on the gene.

5. The genomic display and analysis system of claim 1, wherein, In the gene comparison module between the target species and the species to be compared, a JavaScript function is used to send an asynchronous request to the server to perform a BLAST search. The server queries the sequence to perform a BLAST search and returns the results to the client. Finally, the results returned by the server are parsed and visualized in the results area as a webpage.

6. The genomic display and analysis system of claim 5, wherein, The BLAST module in the gene comparison module between the target species and the species to be compared includes blastn, blastp, blastx, tblastn, and tblastx. The alignment word length, score matrix, and gap penalty are set as follows: blastn program, with a default word length of 11, matching and mismatch scores of 2 and -3, and gap penalties of 5 for Existence and 2 for Extension; blastp, blastx, and tblastn programs, with a default word length of 6, a score matrix of BLOSUM62, and gap penalties of 11 for Existence and 1 for Extension; and tblastx program, with a default word length of 3 and a score matrix of BLOSUM62.

7. The genomic display and analysis system of claim 6, wherein The BLAST was performed by downloading and installing the NCBI BLAST+ package from the NCBI website, which includes command-line tools for performing BLAST locally; a local database was built using the makeblastdb tool to convert the target biological database into a format that BLAST can search; and a script or tool was written using Python or Bash scripting language, which took the provided sequence as input and called the blastn, blastp, blastx, tblastn, or tblastx commands. Use scripts or tools to parse the output file of BLAST and extract the information to be obtained, including the matched sequence, matching degree, and e-value; present the parsed results in the form of tables or graphs.

8. The genome display and analysis system according to claim 1, characterized in that, In the gene comparison module between the target species and the species to be compared, a program written in the Golang development language is used to call the BLAST tool for sequence alignment and searching. The program is then connected to the genome database system to communicate with the database and use the BLAST tool to compare and search sequences.

9. The genome display and analysis system according to claim 1, characterized in that, The target species is Pichia pastoris GS115, and the species to be compared is Saccharomyces cerevisiae S288C.

10. A method for performing interspecies gene and genome analysis using the genome display and analysis system according to any one of claims 1-8, characterized in that, The method includes the following steps: (1) Obtaining genomic and literature information: downloading genomic data, gene annotation data and research information of the target species from online resources; (2) Gene display: data visualization of the target species at the chromosome level, including gene browser and gene information display; (3) Gene comparison: The genes of the target species screened and analyzed are similar to the genes in the genome of the species to be compared. The gene comparison module integrates NCBI's BLAST tool into a localized BLAST module. (4) Primer design: The primer design is based on a Web architecture and integrates the Primer3 program in the backend. The primer design tool is accessed via the Internet to perform actual primer design and display the designed primer parameters, including primer sequence, primer length, melting temperature, GC content, and a score is given based on the primer parameters.

11. The method according to claim 10, characterized in that, The target species is Pichia pastoris GS115.

12. The method according to claim 10, characterized in that, The species to be compared is Saccharomyces cerevisiae S288C.

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