A gene prediction and identification method, apparatus, device, and storage medium

Abstract

This invention provides a gene prediction and identification method, apparatus, device, and storage medium, belonging to the field of gene annotation and prediction. The method includes: acquiring the gene text to be annotated and a set of promoter-terminator pairs; preprocessing the gene text to generate a raw genome sequence; searching the raw genome sequence for base sequences that fuzzy search matches the set of promoter-terminator pairs to generate a base sequence to be aligned; and comparing the base sequence to be aligned with base sequences in a bioinformatics database based on the BLAST gene alignment method to generate gene prediction and identification results. This invention, by separating base sequences from promoter-terminator pairs and then performing BLAST gene sequence alignment, achieves coarse gene localization followed by BLAST gene sequence alignment, providing a method for predicting new genes, improving alignment efficiency and comprehensiveness, as well as the accuracy and comprehensiveness of gene prediction results.

Description

Technical Field

[0001] This invention relates to the field of gene annotation and gene prediction, and more particularly to a gene prediction and identification method, apparatus, device, and storage medium. Background Technology

[0002] With the development of biological research, understanding the genes of individual organisms has attracted widespread attention, especially gene annotation work after gene sequencing. Genomic sequence alignment analysis is an important branch of molecular biology used to study the similarities and differences between genome sequences, as well as the relationship between genome structure and function.

[0003] Current technologies use ORF identification from the NCBI database to identify genes based on six codon pairs. However, start codon-stop codon pairs may not have promoters to initiate transcription, making translation impossible. Furthermore, some genes produce RNA as a ribozyme, and some even use DNA deoxyribozymes to perform their functions, making accurate and comprehensive identification impossible. Additionally, some international research (Genemark, Gail, and some domestic papers) uses large datasets from databases to feed AI or other algorithms, employing mathematical methods to analyze similarity and predict genes. This approach is highly dependent on databases and produces incomplete gene predictions. Gene alignment primarily involves BLASTing the genome text obtained from gene sequencing against genes in a bioinformatics database. However, directly comparing the entire genome sample obtained from sequencing with a bioinformatics database is a waste of computational power and time. This is because the proportion of gene-related base sequences in the DNA of many eukaryotes is relatively low; for example, coding regions account for only 3.2% of the human genome, and the more complex the eukaryote, the larger the proportion of non-coding regions in its genome. In the BLAST gene alignment process, the coding region is the effective alignment region. Performing BLAST on the non-coding region would obviously waste time and computing power, and delay the diagnosis of possible unknown infectious diseases.

[0004] Therefore, in order to improve the comprehensiveness and accuracy of gene prediction and identification, and to improve the efficiency and comprehensiveness of gene alignment, there is an urgent need for a gene prediction and identification method to predict and identify the genome, and then perform BLAST gene sequence alignment on a gene-by-gene basis. Summary of the Invention

[0005] In view of this, it is necessary to provide a gene prediction and identification method, device, equipment and storage medium to solve the technical problems of low efficiency and comprehensiveness of gene sequence alignment and low accuracy of gene prediction in the prior art due to the cumbersome gene sequence alignment algorithm and the incompleteness of the genes obtained from gene annotation and gene prediction.

[0006] To address the aforementioned problems, in a first aspect, the present invention provides a gene prediction and identification method, comprising:

[0007] Obtain the gene text to be annotated and the set of promoter and terminator pairs, and generate the original genome sequence after preprocessing the gene text to be annotated.

[0008] Find the base sequence in the original genome sequence that matches the set of promoter and terminator pairs in a fuzzy search, and generate the base sequence to be aligned;

[0009] Based on the BLAST gene alignment method, the base sequence to be aligned is compared with the base sequence in the bioinformatics database to generate gene prediction and identification results.

[0010] In one possible implementation, the gene text to be annotated is preprocessed to generate the original genome sequence, including:

[0011] Extract the genomic sequence of the gene text to be annotated to generate the first genomic sequence;

[0012] The first genome sequence is reversed to generate the second genome sequence;

[0013] The first genome sequence and the second genome sequence together form the original genome sequence.

[0014] In one possible implementation, the set of promoter-terminator pairs includes:

[0015] Multiple promoter-terminator pairs;

[0016] Multiple auxiliary positioning regulatory sequence promoter terminator pairs, wherein the auxiliary positioning regulatory sequence promoter terminator pairs are used to add auxiliary positioning regulatory sequences and multiple unknown base characters N before the promoter;

[0017] Multiple repliers copy terminator pairs;

[0018] Among them, auxiliary positioning regulatory sequences include: enhancers, operons, silencers, insulators and transposons, and the number of unknown base characters N is determined by the type of auxiliary positioning regulatory sequence.

[0019] In one possible implementation, based on the set of promoter terminator pairs, a base sequence in the original genome sequence that matches the set of promoter terminator pairs in a fuzzy search is searched to generate a base sequence to be aligned, including:

[0020] Based on the promoter-terminator pair, find the promoter and terminator in the original genome sequence that match the promoter-terminator pair, and separate the first aligned base segment and the first remaining base segment;

[0021] Based on the auxiliary positioning regulatory sequence promoter-terminator pair, the promoter and terminator in the corresponding matching auxiliary positioning regulatory sequence promoter-terminator pair in the original genome sequence are searched to determine the matching genome sequence. The matching gene sequence is then matched and screened again by the number of auxiliary positioning regulatory sequences and unknown base characters N, and the second alignment base segment and the second remaining base segment are separated.

[0022] Based on the replicon replication terminator pair, find the replicon and replication terminator in the original genome sequence that match the replicon replication terminator pair, and separate the third aligned base segment and the third remaining base segment;

[0023] The first remaining base segment, the second remaining base segment, and the third remaining base segment are combined with the repeated similar parts to form the fourth alignment base segment;

[0024] The first, second, third, and fourth alignment segments are merged, and duplicate and similar segments are removed to generate a set of segments to be aligned.

[0025] Based on the set of base segments to be aligned, the base sequences are searched and separated to generate the base sequences to be aligned.

[0026] In one possible implementation, based on the set of base segments to be aligned, a base sequence is searched and isolated to generate a base sequence to be aligned, including:

[0027] Search for uppercase and lowercase letters of the characters A, T, C, and G in the set of base segments to be compared;

[0028] Ignore coordinate numbers and spaces and newlines used in the layout;

[0029] The selected base sequences are classified according to the set of promoter and terminator pairs to generate base sequences to be compared.

[0030] In one possible implementation, based on the BLAST gene alignment method, the base sequence to be aligned is compared with base sequences in a bioinformatics database to generate gene prediction and identification results, including:

[0031] The number of processes is obtained, and the base sequences to be compared are sent to the bioinformatics database in batches according to the number of processes to perform BLAST gene sequence comparison and generate gene prediction and identification results.

[0032] In one possible implementation, the gene prediction and identification results include: most gene prediction and identification results are categorized separately according to promoter type; fully matching gene sequences, similar gene sequences, and non-matching gene sequences; the fully matching gene sequences include references for the matching gene, the species of the organism from which the gene originates, gene sequence information, similarity, gene promoter-terminator pairs, and the number of start and stop positions in the original genome; the similar gene sequences include references for the compared sequences, gene sequence information, similarity, gene promoter-terminator pairs, the number of start and stop positions in the original genome, and non-matching base letters marked in red; the non-matching gene sequences include the start site, stop site, length, gene promoter-terminator pairs, and specific sequence of the non-matching gene sequence in the gene sequencing text.

[0033] Secondly, the present invention also provides a gene sequence prediction and identification device, comprising:

[0034] The data acquisition module is used to acquire the gene text to be annotated and the set of promoter and terminator pairs, and to preprocess the gene text to be annotated to generate the original genome sequence.

[0035] The base sequence search module is used to search for base sequences in the original genome sequence that match the set of promoter and terminator pairs in a fuzzy search, and generate base sequences to be compared.

[0036] The alignment module is used to compare the base sequence to be aligned with the base sequence in the bioinformatics database based on the BLAST gene alignment method, and generate gene prediction and identification results.

[0037] Thirdly, the present invention also provides an electronic device, including a memory and a processor, wherein the memory is used to store programs and data; the processor is coupled to the memory and is used to execute the programs stored in the memory to implement the gene prediction and identification method as described above.

[0038] Fourthly, the present invention also provides a computer storage medium for storing a computer-readable program or instruction, which, when executed by a processor, enables the gene prediction and identification method described above.

[0039] The beneficial effects of this invention include: First, this invention preprocesses the gene text to be annotated, reversing the genomic sequence in the gene text, and merging the original genomic sequence and the reversed genomic sequence into the original genomic sequence. That is, when searching the genomic sequence, gene expression is also searched in reverse, following the direction of gene expression. and This allows for a more comprehensive search. Then, based on promoter and terminator pairs, matching base sequences from the original genome sequence are found. Promoters and terminators are both components of a gene; promoters are located upstream of the coding region, representing the beginning of a gene sequence, while terminators are located downstream, providing a termination signal. Based on promoters and terminators, a gene sequence can be accurately located, and its base sequences can be screened. The base sequences in a gene are the basic units reflecting the genetic information within an organism, including the composition and arrangement of genes. Using promoters and terminators, the gene sequence to be compared can be quickly located, and by screening its base sequences, the required gene sequence can be accurately located, further improving the comparison efficiency and the comprehensiveness and accuracy of gene localization. Finally, the screened base sequences are compared with base sequences in the bioinformatics database using a multi-threaded BLAST gene alignment to generate predictive identification results. This coarse-grained gene alignment is more accurate and comprehensive, with higher comparison efficiency. Attached Figure Description

[0040] To more clearly illustrate the technical solutions in the embodiments of the present invention, the accompanying drawings used in the description of the embodiments will be briefly introduced below. Obviously, the accompanying drawings described below are only some embodiments of the present invention. For those skilled in the art, other drawings can be obtained based on these drawings without creative effort.

[0041] Figure 1 This is a schematic flowchart of an embodiment of a gene prediction and identification method provided by the present invention;

[0042] Figure 2 For the present invention Figure 1 A schematic diagram of an embodiment of S101;

[0043] Figure 3 For the present invention Figure 1 A schematic diagram of an embodiment of S102;

[0044] Figure 4 For the present invention Figure 3 A schematic diagram of an embodiment of S305;

[0045] Figure 5 A schematic diagram of the software operation input interface provided by the present invention;

[0046] Figure 6 This is a schematic diagram of an embodiment of a gene prediction and recognition device provided by the present invention;

[0047] Figure 7 This is a schematic diagram of a scenario of an application device for a gene prediction and identification method provided by the present invention;

[0048] Figure 8 This is a structural block diagram of an embodiment of a gene prediction and recognition device provided by the present invention. Detailed Implementation

[0049] The technical solutions of the embodiments of the present invention will be clearly and completely described below with reference to the accompanying drawings. Obviously, the described embodiments are only a part of the embodiments of the present invention, and not all of them. All other embodiments obtained by those skilled in the art based on the embodiments of the present invention without creative effort are within the scope of protection of the present invention.

[0050] It should be understood that the schematic drawings are not drawn to scale. The flowcharts used in this invention illustrate operations implemented according to some embodiments of the invention. It should be understood that the operations in the flowcharts may be implemented out of order, and steps without logical contextual relationships may be reversed or performed simultaneously. Furthermore, those skilled in the art, guided by the content of this invention, may add one or more other operations to the flowcharts, or remove one or more operations from the flowcharts. Some block diagrams shown in the drawings are functional entities and do not necessarily correspond to physically or logically independent entities. These functional entities may be implemented in software, in one or more hardware modules or integrated circuits, or in different network and / or processor devices and / or microcontroller devices.

[0051] In the description of the embodiments of the present invention, unless otherwise stated, "and / or" describes the relationship between associated objects, indicating that there can be three relationships, for example: A and / or B can represent three cases: A exists alone, A and B exist simultaneously, and B exists alone.

[0052] The terms "first," "second," etc., used in the embodiments of this invention are for descriptive purposes only and should not be construed as indicating or implying their relative importance or implicitly specifying the number of technical features indicated. Therefore, a technical feature defined with "first" or "second" may explicitly or implicitly include at least one of that feature.

[0053] In this document, the term "embodiment" means that a particular feature, structure, or characteristic described in connection with an embodiment may be included in at least one embodiment of the invention. The appearance of this phrase in various places throughout the specification does not necessarily refer to the same embodiment, nor is it a separate or alternative embodiment mutually exclusive with other embodiments. It will be explicitly and implicitly understood by those skilled in the art that the embodiments described herein can be combined with other embodiments.

[0054] Before describing the embodiments, the relevant terms are defined as follows:

[0055] BLAST gene alignment (Basic Local Alignment Search Tool): A search tool based on local alignment algorithms, it is a commonly used software tool in bioinformatics. It can compare the input nucleic acid or protein sequence with known sequences in the database to obtain information such as sequence similarity, thereby determining the origin or evolutionary relationship of the sequence.

[0056] Base sequence: refers to the sequence of bases in DNA. There are four types of bases: adenine (A), thymine (T), cytosine (C), and guanine (G).

[0057] This invention provides a gene prediction and identification method, apparatus, device, and storage medium, which are described in detail below.

[0058] This invention provides a gene prediction and identification method, the flowchart of which is shown below. Figure 1 As shown, the gene prediction and identification method includes:

[0059] Step S101: Obtain the gene text to be annotated and the set of promoter and terminator pairs, and preprocess the gene text to be annotated to generate the original genome sequence;

[0060] Step S102: Locate the base sequence in the original genome sequence that matches the set of promoter and terminator pairs in a fuzzy search, and generate the base sequence to be aligned;

[0061] Step S103: Based on the BLAST gene alignment method, the base sequence to be aligned is compared with the base sequence in the bioinformatics database to generate gene prediction and identification results.

[0062] It should be noted that promoters and terminators are components of a gene. Promoters control the initiation time and degree of gene expression or transcription. Promoters are like switches that determine when gene activity begins. Promoters are located in the non-coding region upstream of the coding region. Terminators provide termination information and are responsible for terminating transcription. They are located downstream of the gene. Promoters and terminators work together to ensure that the gene is expressed at the right time, in the right place, and to the appropriate degree.

[0063] It should be further explained that the base sequence is the basic unit reflecting the genetic information in an organism, reflecting the composition and arrangement of genes. The base sequence is the core carrier of genetic information. By comparing and analyzing the base sequence, we can accurately, comprehensively and efficiently compare, analyze, predict and identify the genome sequence.

[0064] Compared with existing technologies, the gene prediction and identification method provided in this embodiment first obtains the gene text to be annotated and a set of promoter and terminator pairs, and preprocesses the gene text to be annotated to generate a raw genome sequence; then, based on the set of promoter and terminator pairs, it searches for base sequences in the raw genome sequence that match the set of promoter and terminator pairs through fuzzy search, generating a base sequence to be aligned; finally, based on the BLAST gene alignment method, it compares the base sequence to be aligned with base sequences in a bioinformatics database to generate gene prediction and identification results. This invention finds matching base sequences in the genome sequence based on promoter and terminator pairs. The promoter can accurately locate the beginning of a gene sequence, and the terminator can accurately locate the end of that gene sequence. Based on the promoter and terminator, the genome sequence to be annotated can be accurately located, and the base sequence of that gene sequence can be screened, further improving the comprehensiveness and accuracy of gene localization prediction and identification, as well as the efficiency and comprehensiveness of gene alignment.

[0065] This invention uses promoter-terminator pairs to find matching base sequences in the genome sequence, which can accurately locate the gene sequence to be aligned and screen out the base sequence of the gene segment, thereby improving the efficiency and comprehensiveness of gene alignment. This coarse localization of genes before BLAST also has the same accuracy and comprehensiveness in the gene prediction and identification process.

[0066] In some embodiments of the present invention, such as Figure 2 As shown, Figure 2 Provided by the present invention Figure 1 A schematic flowchart of an embodiment of step S101 includes:

[0067] S201. Extract the genomic sequence of the gene text to be annotated to generate the first genomic sequence;

[0068] S202. Reverse the first genome sequence to generate the second genome sequence;

[0069] S203, the first genome sequence and the second genome sequence constitute the original genome sequence.

[0070] Specifically, genome sequences are directional, with 3' and 5' ends at both ends of the gene. In most species, the 5' end is the gene's starting point, and the 3' end is the gene's ending point, meaning expression occurs in the 5'→3' direction. However, in a few species, gene expression sometimes occurs in the 3'→5' direction, therefore, a reverse search is necessary when searching the genome sequence.

[0071] This invention preprocesses the gene text to be annotated, reversing the genomic sequence in the gene text. The original genomic sequence and the reversed genomic sequence are then merged into the original genomic sequence. That is, when searching the genomic sequence, since gene expression can occur in both forward and reverse directions, a reverse search is required simultaneously, following the principle that gene expression direction... and This allows for a more comprehensive range of gene searches.

[0072] In some embodiments of the present invention, the set of promoter-terminator pairs includes:

[0073] Multiple promoter-terminator pairs;

[0074] Multiple auxiliary positioning regulatory sequence promoter terminator pairs, wherein the auxiliary positioning regulatory sequence promoter terminator pairs are used to add auxiliary positioning regulatory sequences and multiple unknown base characters N before the promoter;

[0075] Multiple copying termination pairs;

[0076] Among them, auxiliary positioning regulatory sequences include: enhancers, operons, silencers, insulators, and transposons. The number of unknown base characters N is determined by the type of auxiliary positioning gene regulatory sequence.

[0077] It should be noted that there may be multiple promoter-terminator pairs or only one, but there must be at least one; there may also be only one or none of multiple auxiliary positioning and regulatory sequence promoter-terminator pairs; there may also be only one or none of multiple replicon replication-terminator pairs.

[0078] Specifically, as shown in Table 1 below, one promoter can correspond to multiple terminators, and one terminator can also correspond to multiple promoters. Human cells, as hosts for viruses that infect humans, provide transcription-related enzymes for these viruses. Therefore, viruses are usually similar to or identical to human promoter and terminator motifs. Prokaryotes and eukaryotes also have their corresponding promoter and terminator motifs. Therefore, although the specific promoter and terminator sequences of pathogenic microorganisms cannot be confirmed before BLAST, they often do not exceed the finite number of pairings listed in the table above. Based on the known phylogenetic tree branches, the promoter conserved regions and terminator pairs assigned to them can be entered according to the table above when inputting promoter and terminator pairs.

[0079] Table 1. Basic sequences of promoters and terminators in humans, prokaryotes, and eukaryotes.

[0080]

[0081] It should be noted that enhancers are DNA sequences located far from the transcription start site, determining the spatiotemporal specificity of gene expression and enhancing promoter transcriptional activity; their function is usually independent of direction and distance. Operants are units of transcription that occur discontinuously and in segments; each transcribed segment can be considered a transcription unit, called an operon, which includes several structural genes and an upstream regulatory sequence. Silencers are negative regulatory elements found in some genes; when they bind to specific protein factors, they repress gene transcription. Insulators are regulatory sequences located between the promoter and positive regulatory elements (enhancers) or negative regulatory factors (heterochromatin); their function is to prevent other regulatory elements from activating or inactivating genes. Transposons are mobile DNA sequences that can independently replicate in an organism's genome or jump from one location to another, exhibiting autonomy, mobility, and randomness in insertion sites. Replicons are functional units that independently complete DNA replication; conventionally, the distance between two adjacent start sites is defined as one replicon. Eukaryotes use multiple replicons for replication.

[0082] Specifically, such as Figure 5 As shown, Figure 5 The present invention provides a schematic diagram of the software operation input interface. After inputting a promoter-terminator pair on the page, if it is necessary to search for multiple promoter-terminator pairs, clicking the "Add" button allows you to input the promoter-terminator pair to be searched for again. Adding a promoter-terminator pair is done in the same way. Multiple auxiliary positioning and control sequence promoter-terminator pairs are added by clicking the "Add" button and inputting an auxiliary positioning and control sequence promoter-terminator pair or a copying-terminator pair.

[0083] This embodiment uses promoter-terminator pairs, supplemented by replicons, enhancers, silencers, insulators, operons, and transposons to locate genomic sequences. Promoters and terminators are both components of a gene. Promoters are located upstream of the gene coding region, representing the beginning of a gene sequence, while terminators are located downstream of the gene coding region, providing a termination signal. By locating gene sequences based on promoters and terminators, and with the assistance of other gene locators, the gene sequence to be compared can be located more quickly and accurately.

[0084] In some embodiments of the present invention, such as Figure 3 As shown, Figure 3 Provided by the present invention Figure 1 A schematic flowchart of an embodiment of step S102 includes:

[0085] S301. Based on the promoter-terminator pair, find the promoter and terminator in the original genome sequence that match the promoter-terminator pair, and separate the first aligned base segment and the first remaining base segment;

[0086] S302. Based on the auxiliary positioning regulatory sequence promoter-terminator pair, find the promoter and terminator in the corresponding matching auxiliary positioning regulatory sequence promoter-terminator pair in the original genome sequence, determine the matching genome sequence, and perform matching screening on the matching gene sequence again by the number of auxiliary positioning regulatory sequences and unknown base characters N, and separate the second alignment base segment and the second remaining base segment.

[0087] S303. Based on the replicon replication terminator pair, find the replicon and replication terminator in the original genome sequence that match the replicon replication terminator pair, and separate the third aligned base segment and the third remaining base segment;

[0088] S304, the first remaining base segment, the second remaining base segment and the third remaining base segment are combined with the repeated similar parts to form the fourth alignment base segment;

[0089] S305. Merge the first alignment base segment, the second alignment base segment, the third alignment base segment, and the fourth alignment base segment, and remove duplicate and similar base segments to generate a set of base segments to be aligned.

[0090] S306. Based on the set of base segments to be compared, search and separate the base sequences to generate the base sequences to be compared.

[0091] It should be noted that the auxiliary positioning regulatory sequence in the promoter-terminator pair is an enhancer, silencer, insulator, operon, or transposon. At the same time, the number of unknown base characters N is determined according to the type of regulatory sequence in the basic conserved region of the regulatory sequence. When the specific base class is uncertain, the character N is used to replace the base. Multiple characters N represent multiple bases from A, T, C, and G.

[0092] This invention enables rapid and accurate localization of the base segment to be aligned based on the promoter and terminator. The segment to be aligned is defined as the beginning of the matched promoter and the end of the matched terminator. Using the auxiliary localization regulatory sequence promoter-terminator pair, the matching promoter and terminator are first located. Then, the base segment is further filtered based on the auxiliary localization regulatory sequence and the number of unknown base characters N. This base segment must satisfy the condition that the N unknown bases before the promoter are matched auxiliary localization regulatory sequences, where N is an unknown base. The method involves identifying replicons and replication terminators in the original genome sequence that match the replicon replication terminator pair. The sequence from the start of the replicon to the end of the replication terminator represents the matched base segment for alignment. Simultaneously, the matched base segment divides the unmatched sequence into multiple segments, merges the unmatched segments with the matched segments, and removes repetitive and similar segments to generate the final set of base segments to be aligned with prior databases. This embodiment can quickly and accurately locate the gene sequence to be aligned, improving the efficiency of gene alignment and the accuracy of gene prediction.

[0093] In some embodiments of the present invention, such as Figure 4 As shown, Figure 4 Provided by the present invention Figure 3 Step S205 is a flowchart illustrating an embodiment of the steps, including:

[0094] S401. Search the set of base segments to be compared for uppercase and lowercase letters containing the characters A, T, C, and G;

[0095] S402, Ignore coordinate numbers and spaces and newlines used in typesetting;

[0096] S403. The selected base sequences are classified according to the set of promoter and terminator pairs to generate base sequences to be compared.

[0097] It should be noted that there are four types of bases: adenine (A), thymine (T), cytosine (C), and guanine (G). They are important components of nucleic acids in living organisms. Through specific combinations and pairings, they construct the genetic information of living organisms. The base sequence is the basic unit reflecting the genetic information in living organisms, the composition and arrangement of genes. By analyzing the base sequence, we can comprehensively and accurately understand the information of genes.

[0098] This invention isolates base sequences from genome sequences and classifies the selected base sequences according to promoter and terminator pairs to facilitate subsequent alignment, thereby improving the efficiency of genome sequence alignment and enhancing the comprehensiveness and accuracy of gene localization.

[0099] In some embodiments of the present invention, based on the BLAST gene alignment method, the base sequence to be aligned is compared with the base sequences in a bioinformatics database to generate gene prediction and identification results, including:

[0100] The number of processes is obtained, and the base sequences to be compared are sent to the bioinformatics database in batches according to the number of processes to perform BLAST gene sequence comparison and generate gene prediction and identification results.

[0101] It should be noted that the bioinformatics database used in this embodiment is the National Center for Bioinformatics (NCBI) and the China National Gene Bank (CNGB) online database. Other bioinformatics databases can also be used for comparison. The CNGB and NCBI online databases have reserved BLAST interfaces. Automatically initiating multiple BLAST requests to the database requires a certain amount of computing power. Therefore, the number of processes is reasonably adjusted according to the computing power of the software system. Based on the number of processes, the separated base sequences to be compared are sent to the CNGB and NCBI online databases in batches according to the number of processes for BLAST comparison.

[0102] In some embodiments of the present invention, the gene prediction and identification results include: the gene prediction and identification results are categorized separately according to the type of promoter; completely matching gene sequences, similar gene sequences, and non-matching gene sequences; the completely matching gene sequences include references for the matching gene, the species of the organism from which the gene originates, gene sequence information, similarity, gene promoter terminator pairs, and the number of start and stop positions in the original genome; the similar gene sequences include references for the compared sequences, gene sequence information, similarity, gene promoter terminator pairs, the number of start and stop positions in the original genome, and non-matching base letters are marked in red; the non-matching gene sequences include the start site, stop site, length, gene promoter terminator pairs, and specific sequence of the non-matching gene sequence in the gene sequencing text.

[0103] Specifically, the gene prediction and identification results are ultimately saved in compressed files and categorized into different directories according to promoter type for gene species, organ origin, and gene function classification. During the comparison process, a matching similarity threshold is set, ranging from 50% to 20%. In this embodiment, the optimal threshold of 30% is selected. When there are more than 10 gene sequences with a similarity greater than or equal to 30%, the ten gene sequences with the highest similarity are selected, among which gene sequences with 100% similarity are considered completely matched gene sequences, other gene sequences are considered similar gene sequences, and gene sequences with a similarity less than 30% are considered unmatched gene sequences. When there are fewer than 10 gene sequences with a similarity greater than or equal to 30%, the ten gene sequences with the highest similarity are selected based on the overall similarity, among which those with 100% similarity are considered completely matched gene sequences, other gene sequences are considered similar gene sequences, and gene sequences with a similarity less than 30% are considered unmatched gene sequences. Gene sequences with 100% similarity are considered perfectly matched, others are considered similar, and sequences with zero similarity are considered mismatched. For perfectly matched sequences, relevant references, gene length, similarity score, individual names and species to which the matched genes belong, and which characters correspond to the sample sequence in the database, the number of characters, gene promoter and terminator pairs, and the start and stop positions in the original genome are displayed. For similar sequences, in addition to the information displayed for perfectly matched sequences, mismatched base letters are highlighted in red. For mismatched sequences, the start and stop sites, length, and specific sequence information in the sample are displayed to facilitate further investigation into whether they are genes and to explore their origin, function, expression mode, and expression location. Detailed annotations are provided to better analyze the gene prediction and identification results.

[0104] To better implement the gene prediction and identification method in the embodiments of the present invention, three application scenarios of the present invention are described below. It should be understood that the following three application scenarios are only applicable to three application scenarios of the present invention and do not constitute a limitation on the application scenarios of the present invention.

[0105] The gene prediction and identification method of the present invention is applied to the search for unknown viral microorganisms. Specific embodiments include: obtaining the gene text to be annotated and promoter / terminator pairs of humans, prokaryotes, or eukaryotes; using the gene prediction and identification method, finding sequences that do not match the database but have regulatory sequence motif markers, and whose positions in the original genome are numerous and adjacent to each other, which is consistent with the situation of viruses multiplying extensively in host cells and integrating genes into the host cell genome or infecting bacteria and fungi. When the pathogenic microorganism is a virus, its promoter / terminator is the same as or similar to that of the host cell. Bacteria, fungi, and host promoter / terminators usually have low similarity due to their far-reaching evolutionary branches. These genes in the genome of the gene text to be annotated may contain non-coding regions in the intermediate space of the original metagenomics, which can be copied to obtain the unknown pathogen.

[0106] The gene prediction and identification method of the present invention is applied to the identification of gene sequences. Specific embodiments include: acquiring the gene text to be annotated and promoter / terminator pairs of humans, prokaryotes, or eukaryotes; using the gene prediction and identification method, finding gene sequences that match the database; the matching result report displays references related to the gene, the length of the gene, and information such as the individual name and species of the gene sequence; it also shows which letters correspond to the sequences in the gene text to be annotated and the sequences in the database, as well as the number of characters, providing sufficient annotation for subsequent research on gene sequences.

[0107] The gene prediction and identification method of the present invention is applied to the identification of new genes resulting from gene mutations. Specific embodiments include: obtaining the gene text to be annotated and promoter / terminator pairs from humans, prokaryotes, or eukaryotes; using the gene prediction and identification method, finding sequences that do not match the database but have regulatory sequence motif markers, and whose positions in the original genome are not abundant and are irregularly dispersed, indicates that the gene sequence conforms to the situation of gene mutation resulting in a new gene, and is a new gene resulting from gene mutation. The expression of the new gene itself is determined by observing the function of known genes with the same promoter and terminator, which determines in which organs and tissues, developmental stages, and biochemical environments it is expressed, because selective gene expression is often determined by regulatory sequences, and consistent regulatory sequences usually indicate consistent expression environments.

[0108] To better implement the gene prediction and identification method in the embodiments of the present invention, based on the gene prediction and identification method, correspondingly, as follows: Figure 6 As shown, this embodiment of the invention also provides a gene prediction and identification device, the gene prediction and identification device 600 comprising:

[0109] The data acquisition module 601 is used to acquire the gene text to be annotated and the set of promoter and terminator pairs, and to preprocess the gene text to be annotated to generate the original genome sequence.

[0110] The base sequence search module 602 is used to search for base sequences in the original genome sequence that match the set of promoter and terminator pairs in a fuzzy search, and generate base sequences to be compared.

[0111] The alignment module 603 is used to align the base sequence to be aligned with the base sequence in the bioinformatics database based on the BLAST gene alignment method, and generate gene prediction and identification results.

[0112] The gene prediction and identification device 600 provided in the above embodiments can realize the technical solutions described in the above gene prediction and identification method embodiments. The specific implementation principles of each module or unit can be found in the corresponding content in the above gene prediction and identification method embodiments, and will not be repeated here.

[0113] This invention provides a device for gene prediction and identification. Figure 7 This is a schematic diagram of a scenario for an embodiment of the gene prediction and identification method application device provided by the present invention. The device includes:

[0114] Client 701 is used for users to input the gene text path to be compared, the set of promoter and terminator pairs, the number of processes, and to display the gene comparison results;

[0115] Server 702 is used to receive input data from the client, search and separate the gene text to be annotated based on the set of promoter and terminator pairs, and perform BLAST gene alignment with the bioinformatics database.

[0116] Specifically, first, the user inputs the gene text path and promoter / terminator pair set for comparison on the client, and can also input the number of processes. Then, the server receives the input gene text path, retrieves the gene text content based on the path, and simultaneously obtains the promoter / terminator pair set. Next, the server searches the gene text content based on the promoter / terminator pair set to isolate matching base sequences. Finally, the matching base sequences are sent to the bioinformatics database in batches according to the number of processes for BLAST gene alignment, generating gene prediction and identification results, which are displayed on the client. Throughout this process, by searching the genome sequence for base sequences using promoter / terminator pairs and auxiliary localization regulatory sequences, and then performing BLAST alignment with the bioinformatics database, this coarse-grained gene localization and base pair separation for gene prediction and identification is more accurate and comprehensive, and the efficiency of gene BLAST alignment is higher.

[0117] It should be understood that the client 701 used in this embodiment of the invention can be a device that includes both receiving and transmitting hardware, that is, a device having receiving and transmitting hardware capable of performing bidirectional communication on a bidirectional communication link. Such a device may include: cellular or other communication devices having a single-line display, a multi-line display, or a cellular or other communication device without a multi-line display. Specifically, the client 701 may be a desktop computer, a portable computer, a network server, a PDA (Personal Digital Assistant), a mobile phone, a tablet computer, a wireless terminal device, a communication device, an embedded device, etc., and this embodiment does not limit the type of client 701.

[0118] In this embodiment of the invention, the server 702 can be a standalone server, a server network, or a server cluster. For example, the server 702 described in this embodiment includes, but is not limited to, a computer, a network host, a single network server, a set of multiple network servers, or a cloud server composed of multiple servers. The cloud server is composed of a large number of computers or network servers based on cloud computing.

[0119] Those skilled in the art will understand that Figure 7 The application environment shown is merely one application scenario of the present invention and does not constitute a limitation on the application scenarios of the present invention. Other application environments may include those that are more specific to the present invention. Figure 7 The number of more or fewer clients shown, for example Figure 7 Only one client is shown in the diagram. It is understood that the application device of this gene prediction and identification method may also include one or more other clients, which are not limited here.

[0120] It should be noted that, Figure 7 The schematic diagram of the application device of the gene prediction and identification method shown is merely an example. The application device and scenario of the gene prediction and identification method described in the embodiments of the present invention are for the purpose of more clearly illustrating the technical solutions of the embodiments of the present invention, and do not constitute a limitation on the technical solutions provided by the embodiments of the present invention. As those skilled in the art will know, with the evolution of the application device of the gene prediction and identification method and the emergence of new business scenarios, the technical solutions provided by the embodiments of the present invention are also applicable to similar technical problems.

[0121] The present invention also provides a gene prediction and identification device, such as... Figure 8 As shown, Figure 8 This is a structural block diagram of an embodiment of the gene prediction and identification device provided by the present invention. The gene sequence alignment device 800 can be a computing device such as a mobile terminal, desktop computer, laptop, handheld computer, and server. The gene prediction and identification device 800 includes a processor 801 and a memory 802, wherein the memory 802 stores a gene prediction and identification program 803.

[0122] In some embodiments, memory 802 may be an internal storage unit of a computer device, such as a hard disk or memory. In other embodiments, memory 802 may be an external storage device of a computer device, such as a plug-in hard disk, smart media card (SMC), secure digital card (SD), flash card, etc. Further, memory 802 may include both internal and external storage units of the computer device. Memory 802 is used to store application software and various types of data installed on the computer device, such as program code for installing the computer device. Memory 802 can also be used to temporarily store data that has been output or will be output. In one embodiment, gene prediction and identification program 803 may be executed by processor 801 to implement the gene prediction and identification method, apparatus, device, and storage medium of the various embodiments of the present invention.

[0123] In some embodiments, processor 801 may be a central processing unit (CPU), a microprocessor, or other data processing chip, used to run program code stored in memory 802 or process data, such as executing a gene prediction and identification program.

[0124] Those skilled in the art will understand that all or part of the processes in the methods of the above embodiments can be implemented by a computer program instructing related hardware. The computer program can be stored in a non-volatile computer-readable storage medium, and when executed, it can include the processes of the embodiments of the above methods. Any references to memory, storage, databases, or other media used in the embodiments provided in this application can include non-volatile and / or volatile memory. Non-volatile memory can include read-only memory (ROM), programmable ROM (PROM), electrically programmable ROM (EPROM), electrically erasable programmable ROM (EEPROM), or flash memory. Volatile memory can include random access memory (RAM) or external cache memory. By way of illustration and not limitation, RAM is available in various forms, such as static RAM (SRAM), dynamic RAM (DRAM), synchronous DRAM (SDRAM), dual data rate SDRAM (DDRSDRAM), enhanced SDRAM (ESDRAM), synchronous link DRAM (SLDRAM), Rambus direct RAM (RDRAM), direct memory bus dynamic RAM (DRDRAM), and memory bus dynamic RAM (RDRAM), etc.

[0125] The gene prediction and identification method, apparatus, device, and storage medium provided by the present invention have been described in detail above. Specific examples have been used to illustrate the principles and implementation methods of the present invention. The description of the above embodiments is only for the purpose of helping to understand the method and core ideas of the present invention. At the same time, for those skilled in the art, there will be changes in the specific implementation methods and application scope based on the ideas of the present invention. Therefore, the content of this specification should not be construed as a limitation of the present invention.

Claims

1. A method for genetic prediction identification, characterized in that, The method comprises the following steps: obtain a gene text to be annotated and a promoter-terminator pair set, and generate an original genome sequence after preprocessing the gene text to be annotated; the promoter-terminator pair set comprises: a plurality of promoter-terminator pairs; a plurality of auxiliary positioning regulatory sequence promoter-terminator pairs, which are used to add an auxiliary positioning regulatory sequence before a promoter and a plurality of unknown base characters N; a plurality of replicon replication terminator pairs; wherein the auxiliary positioning regulatory sequence comprises: an enhancer, an operator, a silencer, an insulator, and a transposon, and the number of unknown base characters N is determined by the type of the auxiliary positioning regulatory sequence; find base sequences in the original genome sequence that match the fuzzy search of the promoter-terminator pair set to generate a base sequence to be aligned, comprising: according to the promoter-terminator pair, find the promoter and terminator in the original genome sequence that match the promoter-terminator pair, separate out a first aligned base segment and a first remaining base segment; according to the auxiliary positioning regulatory sequence promoter-terminator pair, find the promoter and terminator in the original genome sequence that match the auxiliary positioning regulatory sequence promoter-terminator pair, determine the matched genome sequence, and perform matching screening on the matched gene sequence again through the number of auxiliary positioning regulatory sequences and unknown base characters N, separate out a second aligned base segment and a second remaining base segment; according to the replicon replication terminator pair, find the replicon and replication terminator in the original genome sequence that match the replicon replication terminator pair, separate out a third aligned base segment and a third remaining base segment; merge and repeat similar parts of the first remaining base segment, the second remaining base segment, and the third remaining base segment to form a fourth aligned base segment; merge the first aligned base segment, the second aligned base segment, the third aligned base segment, and the fourth aligned base segment, and remove repeated and similar base segments to generate a base sequence to be aligned; based on the BLAST gene alignment method, align the base sequence to be aligned with the base sequence in the biological information database to generate a gene prediction recognition result.

2. The method of claim 1, wherein the genetic prediction comprises, The method for generating an original genome sequence after preprocessing the gene text to be annotated comprises the following steps: extract the genome sequence of the gene text to be annotated to generate a first genome sequence; reverse the first genome sequence to generate a second genome sequence; the first genome sequence and the second genome sequence form the original genome sequence.

3. The method of claim 2, wherein the genetic prediction comprises, According to the base sequence to be aligned, search and separate out the base sequence to generate the base sequence to be aligned, comprising: search for capital letters and small letters with characters A, T, C, and G in the base sequence to be aligned; ignore coordinate numbers and space symbols and line feed symbols used for layout; classify the screened base sequence according to the promoter-terminator pair set to generate the base sequence to be aligned.

4. The method of claim 3, wherein the genetic prediction is identified by, based on the BLAST gene alignment method, align the base sequence to be aligned with the base sequence in the biological information database to generate a gene prediction recognition result, comprising: The process number is obtained, and the to-be-compared base sequence is sent to a biological information database for BLAST gene sequence comparison in batches according to the process number, to generate a gene prediction and recognition result.

5. The method of claim 4, wherein the genetic prediction comprises, The gene prediction and recognition result includes: the gene prediction and recognition result is classified according to the category of the promoter; a completely matched gene sequence, a similar gene sequence and a non-matched gene sequence; the completely matched gene sequence includes a reference of a matched gene, a species of a biological source of the gene, gene sequence information, similarity, a gene promoter terminator pair and start and end positions in a primary genome; the similar gene sequence includes a reference of a compared sequence, gene sequence information, similarity, a gene promoter terminator pair, start and end positions in a primary genome and a non-matched base letter mark in red; and the non-matched gene sequence includes a start position, an end position, a length, a gene promoter terminator pair and a specific sequence of a non-matched gene sequence in a gene sequencing text.

6. A gene prediction recognition apparatus characterized by comprising: The method comprises: an acquisition data module, configured to acquire a to-be-annotated gene text and a promoter terminator pair set, and generate a primary genome sequence after preprocessing the to-be-annotated gene text; the promoter terminator pair set includes: a plurality of promoter terminator pairs; a plurality of auxiliary positioning and regulation sequence promoter terminator pairs, the auxiliary positioning and regulation sequence promoter terminator pairs being used to add an auxiliary positioning and regulation sequence before a promoter and a plurality of unknown base characters N; and a plurality of replicon replication terminator pairs; wherein the auxiliary positioning and regulation sequence includes an enhancer, an operator, a silencer, an insulator and a transposon, and the number of unknown base characters N is determined according to the type of the auxiliary positioning and regulation sequence; a base sequence searching module, configured to search for a base sequence matched with the promoter terminator pair set in the primary genome sequence, to generate a to-be-compared base sequence, including: searching for a promoter and a terminator matched with the promoter terminator pair in the primary genome sequence according to the promoter terminator pair, to separate a first compared base segment and a first remaining base segment; searching for a promoter and a terminator matched with the auxiliary positioning and regulation sequence promoter terminator pair in the primary genome sequence according to the auxiliary positioning and regulation sequence promoter terminator pair, to determine a matched genome sequence, to perform matching and screening on the matched genome sequence again through the number of auxiliary positioning and regulation sequences and unknown base characters N, to separate a second compared base segment and a second remaining base segment; searching for a replicon and a replication terminator matched with the replicon replication terminator pair in the primary genome sequence according to the replicon replication terminator pair, to separate a third compared base segment and a third remaining base segment; combining and repeating similar parts of the first remaining base segment, the second remaining base segment and the third remaining base segment to form a fourth compared base segment; combining the first compared base segment, the second compared base segment, the third compared base segment and the fourth compared base segment, and removing repeated and similar base segments, to generate a to-be-compared base segment set; searching for and separating a base sequence from the to-be-compared base segment set according to the to-be-compared base segment set, to generate the to-be-compared base sequence. The comparison module is configured to compare the base sequence to be compared with base sequences in a bioinformatics database based on a BLAST gene comparison method to generate a gene prediction recognition result.

7. A gene prediction recognition device characterized by comprising: The computer program is stored in the memory and is executed by the processor to implement the steps of the gene prediction recognition method according to any one of claims 1 to 5.

8. A storage medium, characterized by The storage medium stores computer program instructions, which, when executed by a computer, cause the computer to perform the gene prediction recognition method according to any one of claims 1 to 5.

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