A method and system for fast annotation of genomic sequencing data based on windowed mapping

Abstract

This invention discloses a rapid annotation method and system for genome sequencing data based on window mapping, belonging to the field of bioinformatics. First, this invention constructs mapping values ​​for the start and end sites of all functional components, as well as the start and end points of window mappings within those functional components. An index file is then built using these mapping values. For the sites to be annotated, mapping values ​​are also obtained. The index file is then searched for mapping values. If a site falls between the start and end window mapping values ​​of a specific functional component, it is further determined whether all sites to be annotated fall between the start and end sites of that functional component, thus allowing for annotation. Using this invention, the efficiency of the annotation search can be greatly improved, while reducing the time and computational costs of annotation.

Description

Technical Field

[0001] This invention belongs to the field of bioinformatics technology, specifically relating to a method and system for rapid annotation of genome sequencing data based on window mapping. Background Technology

[0002] Next-generation sequencing (NGS), also known as high-throughput sequencing, is a sequencing-by-synthesis technology developed based on PCR and gene chips. The main characteristics of high-throughput sequencing technology are: short read lengths, high throughput, and high accuracy. Compared to first-generation sequencing, high-throughput sequencing significantly reduces costs while maintaining high accuracy and drastically reducing sequencing time. Currently, high-throughput sequencing is widely used in whole-omics applications, such as: reference transcriptome sequencing, resequencing, DNA methylation sequencing, m6A methylation sequencing, and single-cell sequencing.

[0003] DNA methylation is a major epigenetic modification that can alter genetic expression without changing the DNA sequence, playing a crucial role in regulating gene expression and chromatin conformation. DNA methylation primarily forms 5-methylcytosine (5-mC) and small amounts of N6-methylpurine (N6-mA) and 7-methylguanine (7-mG). Generally, methylated DNA mainly refers to 5-methylcytosine (5-mC). In mammalian cells, methylation mainly occurs on the cytosine of CG dinucleotides, while plant cells exhibit a large proportion of non-CG (CHH, CHG, where H represents A, C, T) methylation. 5-methylcytosine (5-mC) is converted to 5-methylcytosine (mC) by DNA methyltransferase (DNMT) catalyzing the use of S-adenosylmethionine (SAM) as a methyl donor.

[0004] Whole-genome bisulphite sequencing (WGBS), combined with bisulfite conversion and next-generation sequencing (NGS) technology, can efficiently detect the methylation status of whole-genome DNA at single-base resolution. Bisulfite treatment deamination converts unmethylated cytosine in DNA to uracil, while methylated cytosine remains unchanged; in the case of PCR amplification of the desired fragment, uracil is completely converted to thymine. High-throughput sequencing of the PCR products and alignment with a reference sequence can then determine whether methylation has occurred at CpG / CHG / CHH sites. WGBS provides a comprehensive and accurate detection of the methylation status of whole-genome DNA, laying the foundation for more in-depth epigenetic regulatory analysis.

[0005] CpG islands in gene promoter regions are normally demethylated, promoting gene transcription, while aberrant methylation leads to transcriptional inactivation. Generally, CpG island methylation results in gene silencing. DNA methylation plays an important role in genomic imprinting; hypermethylation in one of a biallelic gene leads to monoallelic expression.

[0006] Current bioinformatics software lacks a consistent and rapid annotation method for DNA methylation sequencing data in gene structural regions such as promoters, exons, introns, and intergenic regions, as well as for CpG land regions. Summary of the Invention

[0007] To solve at least one of the above-mentioned technical problems, the present invention adopts the following technical solution:

[0008] The first aspect of this invention provides a method for rapid annotation of genome sequencing data based on window mapping, comprising the following steps:

[0009] S1, Create the index file:

[0010] Obtain the start and end sites of the functional component regions of the species from which the sequencing sample originates. For each functional component, obtain the mapping value using formula (1):

[0011]

[0012] Among them, G i This represents the mapping value of the i-th position, where INT indicates taking the integer part, and S i s represents the value of the i-th position. iThe starting point of the window interval to which the i-th site belongs is represented, and W represents the window size, which is determined based on the lengths of all functional component regions of the source species.

[0013] This yields the mapping values ​​of the start and end points of all functional component areas, as well as the mapping values ​​of the start / end points of windows within the functional component areas. The index file is then constructed in the following format:

[0014] Chr SE se function

[0015] Wherein, Chr represents the chromosome location information of the functional component region, S represents the mapping value of the start site of the functional component region or the start point of the window within the functional component region, E represents the mapping value of the end site of the functional component region or the end point of the window within the functional component region, s represents the start site of the functional component region, E represents the end site of the functional component region, and function represents the category of the functional component region.

[0016] S2, obtain the mapping value of the site to be annotated: its site value is Q, and the mapping value G of the site to be annotated is obtained by formula (1).

[0017] S3, search the second and third columns of the index file using the mapping value G obtained in step S2. If for a certain row j, G satisfies S... j ≤G≤E j Further determine whether Q satisfies s j ≤Q≤e j If the condition is met, the site to be annotated can be annotated in the functional component area corresponding to the j-th row.

[0018] In some embodiments of the present invention, the method for determining W is as follows:

[0019] (1) Obtain the lengths of all functional component regions of the source species;

[0020] (2) Obtain the representative value of the length of all functional component areas, and determine the W value based on the representative value.

[0021] In some specific embodiments of the present invention, the representative value is selected from one of the median, mode, mean, quartile, and 3 / 4 quantile, and the W value is the representative value. In other specific embodiments of the present invention, the W value is located between the quartile and the 3 / 4 quantile.

[0022] Here, obtaining the W value is an unexpected discovery of the present invention that can make the post-processing annotation more efficient. Those skilled in the art can also use other methods to select the W value, as long as they do not violate the core idea of ​​the present invention, they should be considered to fall within the protection scope of the present invention.

[0023] In some embodiments of the invention, the source species is a mammal. Preferably, the source species is a human.

[0024] In some embodiments of the present invention, the gene sequencing data refers to DNA methylation sequencing data.

[0025] In some embodiments of the present invention, the functional component region includes a promoter region, an exon region, an intron region, promoter CGIs, intragenic CGIs, 3'transcript CGIs, intergenic CGIs, a repeat region, and a miRNA region.

[0026] Among them, promoter CGIs, intragenic CGIs, 3'transcript CGIs, and intergenic CGIs are defined according to the gene location to which the CGI belongs:

[0027] promoter CGIs -1000bp TSS to +300bp TSS intragenic CGIs +300bp TSS to +300bp TES 3'transcript CGIs -300bp TES to +300bp TES intergenic CGIs -300bp TES to-1000bp next gene's promoter

[0028] A second aspect of this invention provides a rapid annotation system for genome sequencing data based on windowing mapping, comprising the following modules:

[0029] The index library module is used to store index files, wherein the index files are constructed as follows:

[0030] Obtain the start and end sites of the functional component regions of the species from which the sequencing sample originates. For each functional component, obtain the mapping value using formula (1):

[0031]

[0032] Among them, G i This represents the mapping value of the i-th position, where INT indicates taking the integer part, and S i s represents the value of the i-th position. i The starting point of the window interval to which the i-th site belongs is represented, and W represents the window size, which is determined based on the lengths of all functional component regions of the source species.

[0033] This yields the mapping values ​​of the start and end points of all functional component areas, as well as the mapping values ​​of the start / end points of windows within the functional component areas. The index file is then constructed in the following format:

[0034] Chr SE se function

[0035] Wherein, Chr represents the chromosomal location information of the functional component region, S represents the mapping value of the start site of the functional component region or the starting point of the window within the functional component region, E represents the mapping value of the end site of the functional component region or the ending point of the window within the functional component region, s represents the start site of the functional component region, E represents the end site of the functional component region, and function represents the category of the functional component region.

[0036] The input module is used to receive sequencing data, obtain the sites to be annotated, and calculate the index value of the sites to be annotated using formula (1).

[0037] The search module, connected to both the input module and the index module, searches the second and third columns of the index file for the index values ​​of the sites to be annotated obtained by the input module. If for a given row j, G satisfies S... j ≤G≤E j Further determine whether Q satisfies s j ≤Q≤e j If the conditions are met, the site to be annotated can be annotated in the functional component area corresponding to the j-th row.

[0038] The results output module is used to output the annotation results.

[0039] In some embodiments of the present invention, the method for determining W is as follows:

[0040] (1) Obtain the lengths of all functional component regions of the source species;

[0041] (2) Obtain the representative value of the length of all functional component areas, and determine the W value based on the representative value.

[0042] In some specific embodiments of the present invention, the representative value is selected from one of the median, mode, mean, quartile, and 3 / 4 quantile, and the W value is the representative value. In other specific embodiments of the present invention, the W value is located between the quartile and the 3 / 4 quantile.

[0043] In some embodiments of the invention, the source species is a mammal. Preferably, the source species is a human.

[0044] In some embodiments of the present invention, the gene sequencing data refers to DNA methylation sequencing data.

[0045] In some embodiments of the present invention, the functional component region includes a promoter region, an exon region, an intron region, promoter CGIs, intragenic CGIs, 3'transcript CGIs, intergenic CGIs, a repeat region, and a miRNA region.

[0046] Among them, promoter CGIs, intragenic CGIs, 3'transcript CGIs, and intergenic CGIs are defined according to the gene location to which the CGI belongs:

[0047] promoter CGIs -1000bp TSS to +300bp TSS intragenic CGIs +300bp TSS to +300bp TES 3'transcript CGIs -300bp TES to +300bp TES intergenic CGIs -300bp TES to-1000bp next gene's promoter

[0048] Beneficial effects of the present invention

[0049] Compared with the prior art, the present invention has the following beneficial effects:

[0050] The method and system of this invention map the locations of functional components, offering a simple and easy-to-operate approach that significantly improves search and annotation efficiency. For example, using human chromosome 1, the search efficiency can be improved by 497,506 times. The effect is even more pronounced when annotating multiple chromosomes or multiple samples. Attached Figure Description

[0051] Figure 1 The gene location to which CGI belongs is shown.

[0052] Figure 2 A schematic diagram is shown of a site (10540) located in a promoter region ([10300, 13000]).

[0053] Figure 3 A schematic diagram of the rapid genome sequencing data annotation system based on window mapping of the present invention is shown. Detailed Implementation

[0054] Unless otherwise stated, implied from the context, or as is customary in the art, all parts and percentages in this application are based on weight, and all testing and characterization methods used are concurrent with the filing date of this application. Where applicable, any patent, patent application, or disclosure relating to this application is incorporated herein by reference in its entirety, and its equivalent patent families are also incorporated herein by reference, particularly the definitions disclosed in these documents concerning synthetic techniques, product and processing design, polymers, comonomers, initiators, or catalysts in the art. If any definition of a specific term disclosed in the prior art is inconsistent with any definition provided in this application, the definition provided in this application shall prevail.

[0055] The numerical ranges used in this application are approximate values ​​and therefore may include values ​​outside the range unless otherwise stated. A numerical range includes all values ​​from the lower limit to the upper limit, increasing by one unit, provided there is an interval of at least two units between any lower and any higher value. For example, if 100 to 1000 is stated, it means that all individual values, such as 100, 101, 102, etc., are explicitly listed, as well as all subranges, such as 100 to 166, 155 to 170, 198 to 200, etc. For ranges containing values ​​less than 1 or fractions greater than 1 (e.g., 1.1, 1.5, etc.), one unit is appropriately considered as 0.0001, 0.001, 0.01, or 0.1. For ranges containing single digits less than 10 (e.g., 1 to 5), one unit is generally considered as 0.1. These are merely specific examples of what is intended to be expressed, and all possible combinations of values ​​between the listed lowest and highest values ​​are considered to be clearly stated in this application.

[0056] The terms “comprising,” “including,” “having,” and their derivatives do not exclude the presence of any other components, steps, or processes, regardless of whether such other components, steps, or processes are disclosed in this application. To eliminate any doubt, unless expressly stated otherwise, all compositions using the terms “comprising,” “including,” or “having” in this application may contain any additional additives, excipients, or compounds. Conversely, except for those necessary for operational performance, the term “substantially constitutes…” excludes any other components, steps, or processes described below with respect to that term. The term “consisting of…” does not include any components, steps, or processes not specifically described or listed. Unless expressly stated otherwise, the term “or” refers to the individual members listed or any combination thereof.

[0057] To make the technical problems solved by the present invention, the technical solutions and the beneficial effects of the present invention clearer, the present invention will be further described in detail below with reference to the embodiments.

[0058] Example

[0059] The following examples are used to illustrate preferred embodiments of the invention. Those skilled in the art will understand that the techniques disclosed in the examples represent techniques discovered by the inventors that can be used to implement the invention, and therefore can be considered preferred embodiments for implementing the invention. However, those skilled in the art should understand from this specification that many modifications can be made to the specific embodiments disclosed herein, still yielding the same or similar results, without departing from the spirit or scope of the invention.

[0060] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention pertains, and all materials publicly cited herein and referenced by them are incorporated herein by reference.

[0061] Those skilled in the art will recognize, or can learn through routine experimentation, many equivalents of the specific embodiments of the invention described herein. These equivalents will be included in the claims.

[0062] Unless otherwise specified, the experimental methods used in the following examples are conventional methods. Unless otherwise specified, the instruments and equipment used in the following examples are all conventional laboratory instruments and equipment; unless otherwise specified, the experimental materials used in the following examples were all purchased from conventional biochemical reagent stores.

[0063] Example 1: A rapid annotation method for functional components based on DNA methylation sequencing

[0064] 1. Classification and Definition of Genome Functional Components

[0065] A promoter is a DNA sequence to which a protein binds to initiate the transcription of a single RNA transcript from the DNA downstream of the promoter. The RNA transcript may encode a protein (mRNA) or have its own function (such as tRNA or rRNA). The promoter is located near the transcription start site, upstream of the DNA strand (towards the 5' region of the sense strand). Promoters are approximately 100-1000 base pairs long, and their sequence is highly dependent on the gene and transcript, the type or class of RNA polymerase recruited to that site, and the species of organism. The promoter region is the RNA polymerase binding region, and its structure directly affects the efficiency of transcription.

[0066] The transcription start site (TSS) is the base on the DNA strand corresponding to the first nucleotide of the nascent RNA strand, usually a purine. The sequence preceding the start point, at the 5' end, is called upstream, while the sequence following it, at the 3' end, is called downstream. The positions of the bases are generally represented by numbers: the TSS start point is +1, downstream positions are +2, +3…, and upstream positions are -1, -2, -3…

[0067] In this embodiment, the inventors have defined the promoter region based on TSS as a unified annotation standard for subsequent DNA methylation sequencing analysis, as shown in Table 1:

[0068] Table 1. Definition of Startup Subregion

[0069] Startup sub-region promoters -2,200 to +500bp Proximal Proximal(P) -200 to +500bp Mid-range Intermediate (I) -200 to -1,000bp remote Distal(D) -1,000 to -2,200bp

[0070] The relative position and CpG content within the promoter sequence are important factors influencing the degree of promoter methylation, namely the O / E ratio (observed-to-expected CpG ratio). Based on this ratio, the inventors categorized the O / E values ​​of promoter region CpG into three types: low, medium, and high (LCP, ICP, and HCP). The calculation formula is as follows:

[0071]

[0072] Wherein, Num of CpG represents the number of CpG bases, Num of C represents the number of C bases in the sequence, Num of G represents the number of G bases in the sequence, and Total number of Nucleotides in the sequence expresses the total number of bases in the sequence.

[0073] The inventors defined CpG islands (CGIs) according to their gene locations as shown in Table 2:

[0074] Table 2 CGI Definitions

[0075]

[0076]

[0077] The gene location to which CGI belongs is defined as follows: Figure 1 As shown.

[0078] 2. Annotate the functional component regions to which the sequence belongs using the site translation method.

[0079] The inventors align sequencing reads to the genome based on DNA methylation sequencing results, typically outputting the alignment in SAM format. The SAM format includes site location information, with POS indicating the leftmost position of the read on the genome, representing the location of the first base on the genome. Based on this alignment, those skilled in the art need to quickly annotate which functional region of the gene (e.g., promoter region, exon region, intron region) this site is located in, and also confirm whether it is within a CGI / CGI shores region.

[0080] Here, taking the human genome as an example, human chromosome 1 is 249,250,621 bases long. Suppose that some reads are aligned to the 10,540th base position of this chromosome. How to quickly find out whether this position (10,540) belongs to the promoter region through site search has become a major problem in this field.

[0081] Assume that the site falls within the promoter region ([10300, 13000]) of one of the genes (e.g.) Figure 2 As shown, if the annotation is searched by traversing single sites, it would take 10,540 iterations (traversing from the first base) to find the site located in the promoter region of the genome, which is very inefficient.

[0082] 3. The window mapping method is used to annotate the functional component areas to which the sequence belongs.

[0083] To improve the search efficiency of functional annotations, the inventors created a fast annotation window mapping search method, the detailed process of which is as follows:

[0084] (1) First, the inventors used the following formula to create the mapping of functional components of the genome:

[0085]

[0086] Among them, G i This represents the mapping value of the i-th position, where INT indicates taking the integer part, and S i s represents the value of the i-th position. i W represents the starting point of the window slide interval to which the i-th site belongs, and W represents the window size.

[0087] The size of W is determined based on the lengths of all functional element regions of the source species. Specifically:

[0088] (1) Obtain the lengths of all functional component regions of the source species;

[0089] (2) Obtain the representative value of the length of all functional component areas, and determine the W value based on the representative value.

[0090] Taking a person as an example, the representative values ​​are the 1 / 4 quantile and the 3 / 4 quantile, which are 150 and 2000 respectively. A value W is selected between the 1 / 4 quantile and the 3 / 4 quantile; after selection, W = 500.

[0091] Taking the promoter region [10300, 13000] above as an example, the starting site of this promoter region is (10300), S i =10300, according to the windowing method, s i =10000, G i =10300 / 500=20.

[0092] Using the windowing method, we know that the promoter region is located at the termination point of the first window at 10500 (10000+500), and the corresponding index value is: G. j=10500 / 500=21. Following this pattern, the mapping values ​​for the start / end points of other windows within this promoter region are: 11000 / 500=22, 11500 / 500=23, 12000 / 500=24, 12500 / 500=25, 13000 / 500=26. The termination point of this promoter is also the termination point of a window.

[0093] The inventors used this method to create and store the following index for the boot sector, in the following format:

[0094] Chr S E s e function Chr1 20 21 10300 13000 promoter Chr1 21 22 10300 13000 promoter Chr1 22 23 10300 13000 promoter Chr1 23 24 10300 13000 promoter Chr1 25 26 10300 13000 promoter

[0095] Wherein, Chr represents the chromosomal location information of the functional component region, S represents the mapping value of the start site of the functional component region or the starting point of the window within the functional component region, E represents the mapping value of the end site of the functional component region or the ending point of the window within the functional component region, s represents the start site of the functional component region, E represents the end site of the functional component region, and function represents the category of the functional component region. Categories of functional component regions include, but are not limited to: promoter regions, exonic regions, intronic regions, promoter CGIs, intragenic CGIs, 3' transcript CGIs, intergenic CGIs, repeat regions, and miRNA regions.

[0096] A similar index transformation is performed on all known functional components to obtain an index file.

[0097] Using this method, the inventors compressed the original loci. The original loci corresponding to the interval [20,26] are [10000,13000], that is, 3000 loci were stored in 7 loci, which can improve the search efficiency by 429 times. The effect is very obvious for the huge amount of genomic data.

[0098] When annotating, you only need to convert the corresponding index value of the annotated site before you can annotate:

[0099] G k = k / 500

[0100] Among them, G k S represents the mapping value of site k. k The numerical value representing site k.

[0101] When searching, according to G kThe inventor searches the index file for data in the second column (S) and the second column (E). Simultaneously, based on the queried position, the inventor checks if it falls within the interval of the third and fourth columns. If S≤G k ≤E, and s≤S k If ≤e, then site k can be annotated as the corresponding functional component.

[0102] For example, for the locus 10540 mentioned above, the corresponding index value is converted using the above method, and the converted value is as follows:

[0103] G k =10540 / 500=21

[0104] The site satisfies 20≤21≤21 and 10300≤10540≤13000, therefore site k is annotated as a promoter.

[0105] Example 2: Application of a rapid annotation method for functional components based on DNA methylation sequencing

[0106] This embodiment uses chromosome 1 as an example. The sequence of chromosome 1 has a total of 249,250,621 bases. If the traditional site traversal method is used, it would require a maximum of 249,250,621 traversals to find the annotated site. However, using the window mapping search method in Embodiment 1, with W=500, the sequence can be divided into a maximum of 498,502 index values. The site can be found in a maximum of 501 searches, improving the search efficiency by 497,506 times.

[0107] The specific efficiency improvements are compared in Table 3:

[0108] Table 3 Efficiency Comparison

[0109]

[0110] Therefore, it can be seen that the window mapping search method of Example 1 can significantly improve search performance.

[0111] Example 3: A Rapid Annotation System for Genome Sequencing Data Based on Window Mapping

[0112] like Figure 3 As shown, this embodiment provides a system to implement the above-described rapid annotation method. The system includes:

[0113] The index library module is used to store the index files constructed above.

[0114] The input module receives sequencing data, obtains the site Q to be annotated, and calculates the index value G of the site Q using the formula described above.

[0115] The search module, connected to both the input module and the index module, searches the second and third columns of the index file for the index values ​​of the sites to be annotated obtained by the input module. If for a given row j, G satisfies S... j ≤G≤E j Further determine whether Q satisfies s j ≤Q≤e j If the conditions are met, the site to be annotated can be annotated in the functional component area corresponding to the j-th row.

[0116] The results output module is used to output the annotation results.

[0117] All documents mentioned in this invention are incorporated herein by reference as if each document were individually incorporated by reference. Furthermore, it should be understood that after reading the foregoing teachings of this invention, those skilled in the art can make various alterations or modifications to this invention, and these equivalent forms also fall within the scope defined by the appended claims.

Claims

1. A rapid annotation method for genome sequencing data based on window mapping, characterized in that, Includes the following steps: S1, Create the index file: Obtain the start and end sites of the functional component regions of the species from which the sequencing sample originates. For each functional component, obtain the mapping value using formula (1): （1） in, The mapping value representing the i-th position. INT Indicates taking the integer part. This represents the value at the i-th position. The starting point of the window interval to which the i-th site belongs is represented, and W represents the window size, which is determined based on the lengths of all functional component regions of the source species. This yields the mapping values ​​of the start and end points of all functional component areas, as well as the mapping values ​​of the start / end points of windows within the functional component areas. The index file is then constructed in the following format: Chr SE se function Wherein, Chr represents the chromosome location information of the functional component region, S represents the mapping value of the start site of the functional component region or the start point of the window within the functional component region, E represents the mapping value of the end site of the functional component region or the end point of the window within the functional component region, s represents the start site of the functional component region, and function represents the category of the functional component region. S2, obtain the mapping value of the site to be annotated: its site value is Q, and the mapping value G of the site to be annotated is obtained by formula (1). S3, search the second and third columns of the index file using the mapping value G obtained in step S2. If for a certain row j, G satisfies... , Determine if Q satisfies If the condition is met, the site to be annotated can be annotated in the functional component area corresponding to the j-th row.

2. The rapid annotation method for genome sequencing data according to claim 1, characterized in that, The method for determining W is as follows: (1) Obtain the lengths of all functional component regions of the source species; (2) Obtain the representative value of the length of all functional component areas, and determine the W value based on the representative value.

3. The rapid annotation method for genome sequencing data according to claim 2, characterized in that, The representative value is selected from one of the median, mode, mean, 1 / 4 quantile, and 3 / 4 quantile, or the W value is located between the 1 / 4 quantile and the 3 / 4 quantile.

4. The rapid annotation method for genome sequencing data according to claim 1, characterized in that, The source species is a mammal.

5. The rapid annotation method for genome sequencing data according to claim 4, characterized in that, The functional component region includes the promoter region, exon region, intron region, promoter CGIs, intragenic CGIs, 3' transcript CGIs, intergenic CGIs, repeat region, and miRNA region.

6. A rapid annotation system for genome sequencing data based on windowing mapping, characterized in that, Includes the following modules: The index library module is used to store index files, wherein the index files are constructed as follows: Obtain the start and end sites of the functional component regions of the species from which the sequencing sample originates. For each functional component, obtain the mapping value using formula (1): （1） in, The mapping value representing the i-th position. INT Indicates taking the integer part. This represents the value at the i-th position. The i-th site represents the starting point of the windowed region, and W represents the window size, which is determined based on the lengths of all functional component regions of the source species. This yields the mapping values ​​of the start and end points of all functional component areas, as well as the mapping values ​​of the start / end points of windows within the functional component areas. The index file is then constructed in the following format: Chr SE se function Wherein, Chr represents the chromosomal location information of the functional component region, S represents the mapping value of the start site of the functional component region or the starting point of the window within the functional component region, E represents the mapping value of the end site of the functional component region or the ending point of the window within the functional component region, s represents the start site of the functional component region, and function represents the category of the functional component region. The input module is used to receive sequencing data, obtain the sites to be annotated, and calculate the index value of the sites to be annotated using formula (1). The search module, connected to both the input module and the index module, searches the second and third columns of the index file for the index value of the site to be annotated obtained by the input module. If for a given row j, G satisfies... , Determine if Q satisfies If the conditions are met, the site to be annotated can be annotated in the functional component area corresponding to the j-th row. The results output module is used to output the annotation results.

7. The rapid annotation system for genome sequencing data according to claim 6, characterized in that, The method for determining W is as follows: (1) Obtain the lengths of all functional component regions of the source species; (2) Obtain the representative value of the length of all functional component areas, and determine the W value based on the representative value.

8. The rapid annotation system for genome sequencing data according to claim 7, characterized in that, The representative value is selected from one of the median, mode, mean, quartile, and 3 / 4 quartile; or the W value is located between the quartile and the 3 / 4 quartile.

9. The rapid annotation system for genome sequencing data according to claim 6, characterized in that, The source species is a mammal.

10. The rapid annotation system for genome sequencing data according to claim 9, characterized in that, The functional component region includes the promoter region, exon region, intron region, promoter CGIs, intragenic CGIs, 3' transcript CGIs, intergenic CGIs, repeat region, and miRNA region.

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