Virus sequence genome structure and function annotation method and system

Abstract

The invention provides a virus sequence genome structure and function annotation method and system, and the method comprises the steps: recognizing a terminal repetitive sequence in a virus genome sequence, and deleting or retaining the terminal repetitive sequence according to a first parameter set by a user; predicting an open reading frame in the virus genome sequence, and deleting or retaining the open reading frame according to a second parameter set by the user; annotating the virus genome sequence through a blastp tool, identifying an open reading frame with a virus protein function according to the function annotation of the open reading frame, determining virus classification information, and adjusting the direction of the virus genome sequence according to the annotation; and identifying the double-sense virus according to the virus classification information, reserving overlapped open reading frames in different translation frames of the double-sense virus according to the overlapping degree of the tolerant open reading frames set by the user, and preferentially reserving the open reading frames in the same direction. According to the method, efficient and flexible virus genome annotation with higher adaptability is realized.

Description

Technical Field

[0001] The present invention relates to the technical field of gene annotation, and in particular to a method and system for annotating the structure and function of a viral sequence genome. Background Art

[0002] With the rapid development of high-throughput sequencing technology, massive amounts of viral genome data are being generated. The annotation and function prediction of viral genomes have become core tasks in the fields of virology research, viral vaccine development, and drug target identification. The sequence structure and functional annotation of viral genomes not only help reveal the genetic characteristics of viruses, but also help researchers understand the interaction mechanism between viruses and hosts, clarify the classification of viruses, and predict their potential pathogenicity.

[0003] Traditional gene annotation tools such as GeneMarkS, PROKKA and RAST, although they perform well in the annotation of bacteria and eukaryotes, have certain limitations in the annotation of viral genomes. In particular, in the face of the special structures of viral genomes, such as terminal repeat sequences, overlapping characteristics of open reading frames (ORFs), and bidirectional translation of ambiguous viruses, existing annotation tools are often unable to accurately identify and process these structures. In addition, the accuracy and efficiency of viral genome annotation are crucial to downstream functional research. However, existing tools usually show low computational efficiency, insufficient retention flexibility, and inability to adapt to the classification of all viruses when dealing with these special structures.

[0004] Therefore, the current viral genome annotation technology has many limitations and cannot meet the growing needs in the field of viral research. Especially when faced with the special structure and function annotation of viral sequences, more efficient, flexible and adaptable tools are urgently needed. Summary of the invention

[0005] The present invention provides a method and system for annotating the structure and function of a viral sequence genome, so as to solve the defects of the limitation of the annotation technology of the viral genome in the prior art and realize more efficient, flexible and adaptable viral genome annotation.

[0006] The present invention provides a method for annotating the structure and function of a viral sequence genome, comprising:

[0007] By comparing the viral genome sequence itself, identifying the terminal repeat sequence in the viral genome sequence, and deleting or retaining the terminal repeat sequence according to a first parameter set by a user;

[0008] Predicting the open reading frame in the viral genome sequence by using the getORF software, and deleting or retaining the open reading frame according to a second parameter set by the user;

[0009] Annotating the viral genome sequence by using a blastp tool, identifying an open reading frame having a viral protein function according to the functional annotation of the open reading frame in the annotation, determining viral classification information according to the annotation of the open reading frame having a viral protein function, and adjusting the direction of the viral genome sequence according to the annotation;

[0010] Ambiguous viruses are identified according to the virus classification information, and overlapping open reading frames in different translation frames in the viral genome sequence of the ambiguous virus are retained according to the tolerance of the overlap of the open reading frames set by the user, and open reading frames with viral protein functions in the same direction are preferentially retained.

[0011] According to a method for annotating the structure and function of a viral sequence genome provided by the present invention, the terminal repeat sequence includes a tandem repeat sequence and a reverse complementary repeat sequence.

[0012] According to a method for annotating the structure and function of a viral sequence genome provided by the present invention, the first parameter includes whether to remove the terminal repeat sequence, the shortest terminal tandem repeat sequence retention length, and the shortest terminal reverse complementary repeat sequence retention length. Deleting or retaining the terminal repeat sequence according to the first parameter set by the user includes:

[0013] When the value of whether to remove the terminal repeat sequence is TRUE, deleting the tandem repeat sequence and the reverse complementary repeat sequence;

[0014] In the case that the question of whether to remove the terminal repeat sequence is FALSE, determining whether the length of the tandem repeat sequence is less than the shortest terminal tandem repeat sequence retention length, and whether the length of the reverse complementary repeat sequence is less than the shortest terminal reverse complementary repeat sequence retention length;

[0015] If the length of the tandem repeat sequence is less than the retained length of the shortest terminal tandem repeat sequence, the tandem repeat sequence is deleted; otherwise, the tandem repeat sequence is retained;

[0016] In the case where the length of the reverse complementary repeat sequence is less than the retained length of the shortest terminal reverse complementary repeat sequence, the reverse complementary repeat sequence is deleted; otherwise, the reverse complementary repeat sequence is retained.

[0017] According to a method for annotating the structure and function of a viral sequence genome provided by the present invention, after comparing the viral genome sequence itself and identifying the terminal repeat sequence in the viral genome sequence, the method further comprises:

[0018] Determining the position and content of the terminal repeat sequence in the viral genome sequence;

[0019] The position and content of the terminal repeat sequence are visually displayed.

[0020] According to a method for annotating the structure and function of a viral sequence genome provided by the present invention, the open reading frame includes an open reading frame without a start codon and / or a stop codon.

[0021] According to a method for annotating the structure and function of a viral sequence genome provided by the present invention, the second parameter includes whether to retain all found open reading frames and the shortest open reading frame length, and the deleting or retaining the open reading frame according to the second parameter set by the user includes:

[0022] When the whether to keep all found open reading frames is TRUE, all found open reading frames are kept;

[0023] When the question of whether to retain all found open reading frames is FALSE, for the open reading frames in the same translation frame, retain the longest open reading frame, and determine whether the length of the longest open reading frame is less than the length of the shortest open reading frame;

[0024] When the length of the longest open reading frame is less than the length of the shortest open reading frame, the longest open reading frame is deleted; otherwise, the longest open reading frame is retained.

[0025] A method for annotating the structure and function of a viral sequence genome provided by the present invention also includes:

[0026] Based on the annotation of the viral genome sequence, an annotation file in GFF format, a tbl file for submission to NCBI and NGDC, and a GenBank file for local viewing and editing are generated.

[0027] The present invention also provides a viral sequence genome structure and function annotation system, comprising:

[0028] A terminal repeat sequence detection module, used to identify the terminal repeat sequence in the viral genome sequence by comparing the viral genome sequence itself, and delete or retain the terminal repeat sequence according to a first parameter set by a user;

[0029] An open reading frame prediction module, used to predict the open reading frame in the viral genome sequence by using the getORF software, and to delete or retain the open reading frame according to a second parameter set by a user;

[0030] A functional annotation module, used to annotate the viral genome sequence using a blastp tool, identify open reading frames with viral protein functions according to the functional annotations of the open reading frames in the annotations, determine virus classification information according to the annotations of the open reading frames with viral protein functions, and adjust the direction of the viral genome sequence according to the annotations;

[0031] The ambisense virus identification module is used to identify ambisense viruses according to the virus classification information, retain overlapping open reading frames in different translation frames in the viral genome sequence of the ambisense virus according to the tolerance of open reading frame overlap set by the user, and give priority to retaining open reading frames with viral protein functions in the same direction.

[0032] The present invention also provides an electronic device, comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein when the processor executes the program, the method for annotating the structure and function of the viral sequence genome as described above is implemented.

[0033] The present invention also provides a non-transitory computer-readable storage medium having a computer program stored thereon, which, when executed by a processor, implements any of the above-described methods for annotating the structure and function of a viral sequence genome.

[0034] The present invention also provides a computer program product, comprising a computer program, which, when executed by a processor, implements any of the above-mentioned methods for annotating the structure and function of a viral sequence genome.

[0035] The method and system for annotating the genome structure and function of a viral sequence provided by the present invention can automatically identify and process the special structure of the viral genome, including terminal repeat sequences, overlapping characteristics of open reading frames, and bidirectional translation of ambiguous viruses, thereby improving the accuracy of viral genome annotation and showing higher efficiency and flexibility. BRIEF DESCRIPTION OF THE DRAWINGS

[0036] In order to more clearly illustrate the technical solutions in the present invention or the prior art, the following briefly introduces the drawings required for use in the embodiments or the description of the prior art. Obviously, the drawings described below are some embodiments of the present invention. For ordinary technicians in this field, other drawings can be obtained based on these drawings without paying creative work.

[0037] Figure 1 This is one of the flow diagrams of the structure and function annotation method based on the viral genome sequence provided by the present invention;

[0038] Figure 2It is a schematic diagram of the open reading frame prediction results in the structure and function annotation method based on the viral genome sequence provided by the present invention;

[0039] Figure 3 It is a visualized schematic diagram of the terminal repeat sequence of the viral genome in the structure and function annotation method based on the viral genome sequence provided by the present invention;

[0040] Figure 4 This is the second flow chart of the structure and function annotation method based on viral genome sequence provided by the present invention;

[0041] Figure 5 It is a schematic diagram of the structure of the structure and function annotation system based on the viral genome sequence provided by the present invention;

[0042] Figure 6 It is a structural schematic diagram of the electronic device provided by the present invention. DETAILED DESCRIPTION

[0043] In order to make the purpose, technical solution and advantages of the present invention clearer, the technical solution of the present invention will be clearly and completely described below in conjunction with the drawings of the present invention. Obviously, the described embodiments are part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without creative work are within the scope of protection of the present invention.

[0044] In the field of virus-related gene annotation, existing technologies such as GLIMMER and VAPiD are useful in annotating specific viral genomes, but these tools have shortcomings in the following aspects:

[0045] Identification and processing of terminal repeat sequences: Viral genomes often contain terminal repeat sequences (such as tandem repeat sequences and reverse complementary repeat sequences), which play an important role in the evolution and function of viral genomes. Existing tools are often unable to automatically identify and process these repeat sequences, resulting in inaccurate annotation results.

[0046] Prediction and annotation of open reading frames: The common phenomenon of open reading frame overlap in viral genomes is not well handled by existing tools. Especially for ambiguous viruses, existing tools cannot accurately distinguish and retain functional open reading frames in the same direction and in different directions.

[0047] Classification and direction adjustment: Sequence direction adjustment and classification determination after virus annotation depend on the annotation results, but existing tools have limited support for virus classification, cannot automatically adjust sequence direction according to annotation results, and have limited applicability to different viruses.

[0048] Efficiency and flexibility: Existing technologies often take a long time to process viral genomes, especially when dealing with large amounts of data or complex genome structures, and lack flexibility in customizing the retention and discarding of reading frames.

[0049] The present invention provides a method and system for structural and functional annotation based on viral genome sequences, which effectively improves the deficiencies in the prior art.

[0050] Combine the following Figure 1 A method for annotating the structure and function of a viral sequence genome of the present invention is described, comprising:

[0051] Step 101, identifying the terminal repeat sequence in the viral genome sequence by comparing the viral genome sequence itself, and deleting or retaining the terminal repeat sequence according to a first parameter set by a user;

[0052] This embodiment realizes the identification of terminal repeat sequences, and automatically detects whether tandem repeat sequences and reverse complementary repeat sequences exist at the ends of the viral genome sequence through the comparison of the sequences themselves, and flexibly selects to delete or retain these repeat sequences according to the first parameter set by the user.

[0053] Step 102, predicting the open reading frame in the viral genome sequence by using getORF software, and deleting or retaining the open reading frame according to a second parameter set by the user;

[0054] This embodiment achieves flexible retention of open reading frames by predicting all open reading frames in the viral genome sequence through getORF, especially being able to identify open reading frames without start codons or stop codons, and processing these open reading frames. Figure 2 shown.

[0055] The open reading frame can be flexibly selected to be deleted or retained according to the second parameter set by the user, thereby improving the flexibility of the reading frame selection.

[0056] Step 103, annotating the viral genome sequence by using a blastp tool, identifying an open reading frame having a viral protein function according to the functional annotation of the open reading frame in the annotation, determining virus classification information according to the annotation of the open reading frame having a viral protein function, and adjusting the direction of the viral genome sequence according to the annotation;

[0057] This embodiment implements virus function annotation and classification, and uses the blastp tool to perform function annotation on the retained open reading frames to identify open reading frames with virus protein functions. The value Evalue of the virus protein function annotation is identified according to the blastp tool set by the user. For example, the value Evalu of the virus protein function annotation is set to 1e-5, which is 1e-5 by default.

[0058] The smallest classification unit of the virus is determined based on the annotation results of open reading frames with viral protein functions, and the virus classification information is output to improve the accuracy and efficiency of virus classification.

[0059] Diamond can be used to establish the uniport protein database ProtDB, and to establish a corresponding relationship table between the protein ID in the protein database and the virus classification ID. The protein ID is obtained from the annotation of the open reading frame with viral protein function, and the virus classification ID is obtained by searching the relationship table, thereby obtaining the virus classification information.

[0060] In addition, the direction of the viral genome sequence determined by the functional annotation results can be automatically adjusted based on whether it is consistent with the direction of the target sequence to ensure the correctness of the viral genome sequence.

[0061] Step 104, identifying ambiguous viruses according to the virus classification information, retaining overlapping open reading frames in different translation frames in the viral genome sequence of the ambiguous virus according to the tolerance of open reading frame overlap set by the user, and giving priority to retaining open reading frames with viral protein functions in the same direction.

[0062] This embodiment realizes the identification and direction optimization of ambiguous viruses, automatically distinguishes ambiguous viruses according to the virus classification information obtained from the annotation results, and preferentially retains the viral protein open reading frames along the 5'->3' or 3'->5' direction according to the annotation results to ensure the accuracy of the annotation.

[0063] Sort by the total length or total number (by default, the total length) of the open reading frames (ORFs) of the annotated viral proteins in the same direction. If the total length in the 5'->3' direction is greater than the total length in the 3'->5' direction or the total number in the 5'->3' direction is greater than the total number in the 3'->5' direction, the sequence direction does not need to be adjusted; otherwise, the sequence is reverse complemented.

[0064] Based on the tolerance of ORF overlap selected by the user (default 70%), overlapping ORFs in different translation frames are retained. Open reading frames in different translation frames are allowed to overlap to a specified degree, which solves the defect that existing annotation tools cannot handle ORF overlap.

[0065] The intersection of the newly discovered open reading frame and the gap between the known functional protein open reading frame can also be set, such as ORFoverlap=0.1, which means that the default gap must overlap the new open reading frame by a minimum of 10%.

[0066] When annotating the viral genome sequence, this embodiment takes into account the special structure of the viral genome, including terminal repeat sequences, overlapping characteristics of open reading frames, and bidirectional translation of ambiguous viruses, and can automatically identify and process them, thereby improving the accuracy of viral genome annotation and showing higher efficiency and flexibility.

[0067] Based on the above embodiment, the terminal repeat sequence in this embodiment includes a tandem repeat sequence and a reverse complementary repeat sequence.

[0068] Based on the above embodiment, in this embodiment, the first parameter includes whether to remove the terminal repeat sequence, the shortest terminal tandem repeat sequence retention length, and the shortest terminal reverse complementary repeat sequence retention length. Deleting or retaining the terminal repeat sequence according to the first parameter set by the user includes:

[0069] When the value of whether to remove the terminal repeat sequence is TRUE, deleting the tandem repeat sequence and the reverse complementary repeat sequence;

[0070] In the case that the question of whether to remove the terminal repeat sequence is FALSE, determining whether the length of the tandem repeat sequence is less than the shortest terminal tandem repeat sequence retention length, and whether the length of the reverse complementary repeat sequence is less than the shortest terminal reverse complementary repeat sequence retention length;

[0071] If the length of the tandem repeat sequence is less than the retained length of the shortest terminal tandem repeat sequence, the tandem repeat sequence is deleted; otherwise, the tandem repeat sequence is retained;

[0072] In the case where the length of the reverse complementary repeat sequence is less than the retained length of the shortest terminal reverse complementary repeat sequence, the reverse complementary repeat sequence is deleted; otherwise, the reverse complementary repeat sequence is retained.

[0073] Whether to remove terminal repeat sequences removeTR includes whether to remove tandem repeat sequences and reverse complementary repeat sequences. You can set removeTR=TRUE or removeTR=FALSE. The default is not to delete.

[0074] The shortest terminal tandem repeat sequence retention length MIN_LENGTH_DTR can be set to 10, the default is 20bp, and the shortest terminal reverse complementary repeat sequence retention length MIN_LENGTH_ITR can be set to 10, the default is 20bp. Repeat sequences with a length less than 20bp will be deleted.

[0075] On the basis of the above embodiment, in this embodiment, after comparing the viral genome sequence itself and identifying the terminal repeat sequence in the viral genome sequence, the following steps are further included:

[0076] Determining the position and content of the terminal repeat sequence in the viral genome sequence;

[0077] The position and content of the terminal repeat sequence are visually displayed.

[0078] A visualization diagram of the terminal repeat sequence of the viral genome is shown in Figure 3 This embodiment supports visual display of the location and content of repeated sequences, which helps researchers to intuitively understand the structural characteristics of the genome.

[0079] Based on the above embodiments, the open reading frame in this embodiment includes an open reading frame without a start codon and / or a stop codon.

[0080] Based on the above embodiment, the second parameter in this embodiment includes whether to retain all found open reading frames and the shortest open reading frame length, and the deleting or retaining of the open reading frame according to the second parameter set by the user includes:

[0081] When the whether to keep all found open reading frames is TRUE, all found open reading frames are kept;

[0082] When the question of whether to retain all found open reading frames is FALSE, for the open reading frames in the same translation frame, retain the longest open reading frame, and determine whether the length of the longest open reading frame is less than the length of the shortest open reading frame;

[0083] When the length of the longest open reading frame is less than the length of the shortest open reading frame, the longest open reading frame is deleted; otherwise, the longest open reading frame is retained.

[0084] You can set whether to keep all the found open reading frames KeepAllOrff = TRUE or KeepAllOrff = FALSE. The default is not to keep. For open reading frames in the same translation frame, the longest open reading frame is kept.

[0085] Allow users to customize the shortest open reading frame length MinLenORF=200, the default is 200bp, delete open reading frames less than 200bp in length, selectively retain or delete open reading frames, and achieve flexible screening of open reading frames.

[0086] Based on the above embodiment, this embodiment also includes:

[0087] Based on the annotation of the viral genome sequence, an annotation file in GFF format that meets the submission standards of NCBI and NGDC, a tbl file for submission to NCBI and NGDC, and a GenBank file for local viewing and editing are automatically generated.

[0088] This embodiment realizes the generation of standardized file formats, can automatically generate gene annotation files in GFF format, feature files in tbl format, and GenBank files for local viewing and editing, supports direct submission to NCBIgenbank and NGDC-CNCB genbase, and sharing of genome data, greatly simplifying the submission and sharing process of genome data.

[0089] Figure 4 The invention is a flow chart of the structure and function annotation method based on the viral genome sequence. First, the fasta file of the viral genome sequence is input, and the system detects the presence of tandem repeat sequences at both ends of the viral sequence, and deletes them according to the parameters set by the user; then, the system predicts all open reading frames in the genome, and identifies multiple open reading frames with viral protein functions through blastp functional annotation. If the system recognizes that this is an ambiguous virus, the problem of ORF overlap is successfully solved by preferentially retaining the viral protein ORF in the 5'->3' direction. The generated GFF file and tbl file are directly submitted to NCBI through the system, and the entire annotation process only takes a few minutes, which reduces a lot of manual adjustment time compared to traditional annotation tools.

[0090] Compared with the commonly used command line tools PROKKA, GLIMMER, and VAPiD, this system shows higher efficiency and flexibility in processing viral genomes. Traditional tools often require manual intervention when dealing with ambiguous viruses and ORF overlaps, while this system can automatically identify and process them, greatly improving the accuracy of viral genome annotations. In addition, the generated files meet international standards, facilitating the sharing of genomic data.

[0091] Compared with existing tools, this method can significantly shorten the running time when processing large-scale viral genome data. In addition, this method is applicable to all viral sequences and is not limited to specific viral classifications, which enhances the versatility and flexibility of the tool. The operation is simple, and all functional modules are highly integrated, and can be operated with only one line of command.

[0092] The viral sequence genome structure and function annotation system provided by the present invention is described below. The viral sequence genome structure and function annotation system described below and the viral sequence genome structure and function annotation method described above can be referenced to each other.

[0093] like Figure 5As shown, the system includes a terminal repeat sequence detection module 501, an open reading frame prediction module 502, a function annotation module 503 and an ambiguous virus identification module 504, wherein:

[0094] The terminal repeat sequence detection module 501 is used to identify the terminal repeat sequence in the viral genome sequence by comparing the viral genome sequence itself, and delete or retain the terminal repeat sequence according to the first parameter set by the user;

[0095] The open reading frame prediction module 502 is used to predict the open reading frame in the viral genome sequence by using the getORF software, and delete or retain the open reading frame according to the second parameter set by the user;

[0096] The function annotation module 503 is used to annotate the viral genome sequence by using a blastp tool, identify the open reading frames with viral protein functions according to the functional annotations of the open reading frames in the annotations, determine the virus classification information according to the annotations of the open reading frames with viral protein functions, and adjust the direction of the viral genome sequence according to the annotations;

[0097] The ambisense virus identification module 504 is used to identify ambisense viruses according to the virus classification information, retain overlapping open reading frames in different translation frames in the viral genome sequence of the ambisense virus according to the tolerance of open reading frame overlap set by the user, and give priority to retaining open reading frames with viral protein functions in the same direction.

[0098] This embodiment takes into account the special structure of the viral genome when annotating the viral genome sequence, including terminal repeat sequences, overlapping characteristics of open reading frames, and bidirectional translation of ambiguous viruses, and can automatically identify and process them, thereby improving the accuracy of viral genome annotation and showing higher efficiency and flexibility.

[0099] Figure 6 An example of a physical structure diagram of an electronic device is shown in FIG. Figure 6As shown, the electronic device may include: a processor 610, a communication interface 620, a memory 630 and a communication bus 640, wherein the processor 610, the communication interface 620 and the memory 630 communicate with each other through the communication bus 640. The processor 610 may call the logic instructions in the memory 630 to execute the viral sequence genome structure and function annotation method, the method comprising: identifying the terminal repeat sequence in the viral genome sequence, deleting or retaining the terminal repeat sequence according to the first parameter set by the user; predicting the open reading frame in the viral genome sequence, deleting or retaining the open reading frame according to the second parameter set by the user; annotating the viral genome sequence by the blastp tool, identifying the open reading frame with the function of the viral protein according to the functional annotation of the open reading frame, determining the virus classification information, and adjusting the direction of the viral genome sequence according to the annotation; identifying the ambiguous virus according to the virus classification information, retaining the overlapping open reading frames in different translation frames of the ambiguous virus according to the tolerance of the overlap of the open reading frames set by the user, and preferentially retaining the open reading frames in the same direction.

[0100] In addition, the logic instructions in the above-mentioned memory 630 can be implemented in the form of software functional units and can be stored in a computer-readable storage medium when sold or used as an independent product. Based on such an understanding, the technical solution of the present invention, in essence, or the part that contributes to the prior art or the part of the technical solution, can be embodied in the form of a software product, which is stored in a storage medium and includes several instructions for a computer device (which can be a personal computer, a server, or a network device, etc.) to perform all or part of the steps of the method described in each embodiment of the present invention. The aforementioned storage medium includes: various media that can store program codes, such as a USB flash drive, a mobile hard disk, a read-only memory (ROM), a random access memory (RAM), a disk or an optical disk.

[0101] On the other hand, the present invention also provides a computer program product, which includes a computer program, which can be stored on a non-transitory computer-readable storage medium. When the computer program is executed by a processor, the computer can execute the viral sequence genome structure and function annotation method provided by the above methods, which method includes: identifying terminal repeat sequences in the viral genome sequence, deleting or retaining the terminal repeat sequences according to a first parameter set by a user; predicting open reading frames in the viral genome sequence, deleting or retaining the open reading frames according to a second parameter set by the user; annotating the viral genome sequence through a blastp tool, identifying open reading frames with viral protein functions according to the functional annotations of the open reading frames, determining virus classification information, and adjusting the direction of the viral genome sequence according to the annotations; identifying ambiguous viruses according to the virus classification information, retaining overlapping open reading frames in different translation frames of ambiguous viruses according to the tolerance degree of overlap of open reading frames set by the user, and giving priority to retaining open reading frames in the same direction.

[0102] On the other hand, the present invention also provides a non-transitory computer-readable storage medium having a computer program stored thereon, which is implemented when the computer program is executed by the processor to execute the viral sequence genome structure and function annotation method provided by the above-mentioned methods, the method comprising: identifying the terminal repeat sequence in the viral genome sequence, deleting or retaining the terminal repeat sequence according to a first parameter set by the user; predicting the open reading frame in the viral genome sequence, deleting or retaining the open reading frame according to a second parameter set by the user; annotating the viral genome sequence by a blastp tool, identifying the open reading frame with viral protein function according to the functional annotation of the open reading frame, determining the virus classification information, and adjusting the direction of the viral genome sequence according to the annotation; identifying ambiguous viruses according to the virus classification information, retaining the overlapping open reading frames in different translation frames of the ambiguous viruses according to the tolerance degree of overlap of the open reading frames set by the user, and giving priority to retaining the open reading frames in the same direction.

[0103] The system embodiment described above is merely illustrative, wherein the units described as separate components may or may not be physically separated, and the components shown as units may or may not be physical units, that is, they may be located in one place, or they may be distributed on multiple network units. Some or all of the modules may be selected according to actual needs to achieve the purpose of the solution of this embodiment. Those of ordinary skill in the art may understand and implement it without creative work.

[0104] Through the description of the above implementation methods, those skilled in the art can clearly understand that each implementation method can be implemented by means of software plus a necessary general hardware platform, and of course, it can also be implemented by hardware. Based on this understanding, the above technical solution is essentially or the part that contributes to the prior art can be embodied in the form of a software product, and the computer software product can be stored in a computer-readable storage medium, such as ROM / RAM, a disk, an optical disk, etc., including a number of instructions for a computer device (which can be a personal computer, a server, or a network device, etc.) to execute the methods described in each embodiment or some parts of the embodiments.

[0105] Finally, it should be noted that the above embodiments are only used to illustrate the technical solutions of the present invention, rather than to limit it. Although the present invention has been described in detail with reference to the aforementioned embodiments, those skilled in the art should understand that they can still modify the technical solutions described in the aforementioned embodiments, or make equivalent replacements for some of the technical features therein. However, these modifications or replacements do not deviate the essence of the corresponding technical solutions from the spirit and scope of the technical solutions of the embodiments of the present invention.

Claims

1. A method for annotating the structure and function of viral sequence genomes, characterized in that: include: By comparing the viral genome sequence itself, identifying the terminal repeat sequence in the viral genome sequence, and deleting or retaining the terminal repeat sequence according to a first parameter set by a user; Predicting the open reading frame in the viral genome sequence by using the getORF software, and deleting or retaining the open reading frame according to a second parameter set by the user; Annotating the viral genome sequence by using a blastp tool, identifying an open reading frame having a viral protein function according to the functional annotation of the open reading frame in the annotation, determining viral classification information according to the annotation of the open reading frame having a viral protein function, and adjusting the direction of the viral genome sequence according to the annotation; Ambiguous viruses are identified according to the virus classification information, and overlapping open reading frames in different translation frames in the viral genome sequence of the ambiguous virus are retained according to the tolerance of the overlap of the open reading frames set by the user, and open reading frames with viral protein functions in the same direction are preferentially retained.

2. The method for annotation of viral sequence genome structure and function according to claim 1, characterized in that: The terminal repeat sequence includes a tandem repeat sequence and an inverse complementary repeat sequence.

3. The method for annotation of viral sequence genome structure and function according to claim 2, characterized in that: The first parameter includes whether to remove the terminal repeat sequence, the shortest terminal tandem repeat sequence retention length and the shortest terminal reverse complementary repeat sequence retention length. Deleting or retaining the terminal repeat sequence according to the first parameter set by the user includes: When the value of whether to remove the terminal repeat sequence is TRUE, deleting the tandem repeat sequence and the reverse complementary repeat sequence; In the case that the question of whether to remove the terminal repeat sequence is FALSE, determining whether the length of the tandem repeat sequence is less than the shortest terminal tandem repeat sequence retention length, and whether the length of the reverse complementary repeat sequence is less than the shortest terminal reverse complementary repeat sequence retention length; If the length of the tandem repeat sequence is less than the retained length of the shortest terminal tandem repeat sequence, the tandem repeat sequence is deleted; otherwise, the tandem repeat sequence is retained; In the case where the length of the reverse complementary repeat sequence is less than the retained length of the shortest terminal reverse complementary repeat sequence, the reverse complementary repeat sequence is deleted; otherwise, the reverse complementary repeat sequence is retained.

4. The method for annotation of viral sequence genome structure and function according to claim 1, characterized in that: After identifying the terminal repeat sequence in the viral genome sequence by comparing the viral genome sequence itself, the method further includes: Determining the position and content of the terminal repeat sequence in the viral genome sequence; The position and content of the terminal repeat sequence are visually displayed.

5. The method for annotation of viral sequence genome structure and function according to claim 1, characterized in that: The open reading frame includes an open reading frame without a start codon and / or a stop codon.

6. The method for annotation of viral sequence genome structure and function according to claim 1, characterized in that: The second parameter includes whether to retain all found open reading frames and the shortest open reading frame length, and the deletion or retention of the open reading frame according to the second parameter set by the user includes: When the whether to keep all found open reading frames is TRUE, all found open reading frames are kept; When the question of whether to retain all found open reading frames is FALSE, for the open reading frames in the same translation frame, retain the longest open reading frame, and determine whether the length of the longest open reading frame is less than the length of the shortest open reading frame; When the length of the longest open reading frame is less than the length of the shortest open reading frame, the longest open reading frame is deleted; otherwise, the longest open reading frame is retained.

7. The method for annotating the structure and function of a viral sequence genome according to any one of claims 1 to 6, characterized in that: Also includes: Based on the annotation of the viral genome sequence, an annotation file in GFF format, a tbl file for submission to NCBI and NGDC, and a GenBank file for local viewing and editing are generated.

8. A viral sequence genome structure and function annotation system, characterized in that: include: A terminal repeat sequence detection module, used to identify the terminal repeat sequence in the viral genome sequence by comparing the viral genome sequence itself, and delete or retain the terminal repeat sequence according to a first parameter set by a user; An open reading frame prediction module, used to predict the open reading frame in the viral genome sequence by using the getORF software, and to delete or retain the open reading frame according to a second parameter set by a user; A functional annotation module, used to annotate the viral genome sequence using a blastp tool, identify open reading frames with viral protein functions according to the functional annotations of the open reading frames in the annotations, determine virus classification information according to the annotations of the open reading frames with viral protein functions, and adjust the direction of the viral genome sequence according to the annotations; The ambisense virus identification module is used to identify ambisense viruses according to the virus classification information, retain overlapping open reading frames in different translation frames in the viral genome sequence of the ambisense virus according to the tolerance of open reading frame overlap set by the user, and give priority to retaining open reading frames with viral protein functions in the same direction.

9. An electronic device comprising a memory, a processor, and a computer program stored in the memory and executable on the processor, wherein: When the processor executes the program, the method for annotating the structure and function of the viral sequence genome as described in any one of claims 1 to 7 is implemented.

10. A non-transitory computer-readable storage medium having a computer program stored thereon, characterized in that: When the computer program is executed by a processor, the method for annotating the structure and function of a viral sequence genome as claimed in any one of claims 1 to 7 is implemented.

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