KR20030038911A - An Integrated and Automated Processing Method for Deoxyribonucleic Acid Sequence Informations - Google Patents

Abstract

The present invention relates to a method for treating deoxyribonucleic acid base sequence. The method of the present invention inputs base sequence source information, and integrates the base sequence source information into a process such as base calling, vector masking, repeat masking, clustering, contiguous assembly, and the like by a parallel processing method. The sequence information is analyzed for similarity with existing registered genetic information, and the processed sequence information and similarity analysis results are prepared in a database and visualized.

According to the present invention, if processing the sequencing information, it is possible to solve the problem of exposure of information that may be the subject of intellectual property rights that may occur when processing the sequencing information by requesting other specialized processing institutions, according to the processing request Minimize cost and latency, integrate and automate multi-step data processing processes to simplify processing, reduce processing time, and apply graphical user environment to increase the efficiency It is possible to improve the work efficiency in the fields related to the processing and utilization of genetic information because it can be improved, the processing results are immediately stored in the database, and the data can be easily retrieved and reused later.

Description

An Integrated and Automated Processing Method for Deoxyribonucleic Acid Sequence Informations}

The present invention relates to a method for integrating and automating deoxyribonucleic acid sequencing information. In particular, errors and unnecessary data included in the raw data of sequencing information obtained from the sequencing analyzer are removed using a computer and software, and ultimately, The present invention relates to a method of linking various programs used in a series of integration and automation processes from processing a form to a purpose of use and storing it in a database, and a system to which the method is applied.

Recently, the development of genetic engineering is rapidly progressing as the use of a computer in the analysis of deoxyribonucleic acid sequencing information having the genetic information of living organisms rapidly deciphers the vast genetic information.

In general, the raw data of the sequence information obtained from the sequencing analyzer is obtained through a variety of laboratory methods to obtain the sequence information. Due to the nature of the experiment process, the initial data obtained includes various errors and unnecessary data. There may be.

This is due to errors due to the nature of the sequencing analyzer, errors and contamination of the assay results from gene cloning or polymerase chain reaction (PCR), and the preparation of various sequencing. .

In order for sequencing information to be used as valuable genetic information, these errors and unnecessary information must be eliminated, and in a way, a multi-step process using various kinds of computer programs is required.

The processing of the deoxyribonucleic acid sequence information generally includes base calling, vector and host sequence clipping, repeat masking, clustering, and contig assembly. ), Similarity analysis (homology analysis), database storage, etc. A separate program for each purpose is developed and used.

In the conventional process, each process step is not linked, and the programs are operated as separate independent programs, and in most cases, the user does not grasp the existence of a program suitable for step-by-step processing.

In addition, most of the programs used must be executed by directly inputting the program name and many user options on the command line, and the various input / output data types are very difficult to learn how to use. It is not easy to obtain the treatment result.

Therefore, most genetic information workers who do not have the ability to process deoxyribonucleic acid nucleotide sequence information can be subject to intellectual property rights by processing the sequencing information obtained in the course of their work with domestic or foreign institutions. There is a wide range of losses, including the risk of exposing sensitive genetic information, the cost of referrals and the waiting time for processing results.

The purpose of the present invention is to integrate and automate the complex processing of deoxyribonucleic acid sequence information in a pipeline method and to improve the user environment in order to solve the problems of the prior art by the general practitioners involved in the genetic information work It is to provide a method for integrating and automating deoxyribonucleic acid sequence information that can easily, economically and safely process their genetic information.

1 is a flow chart of the integrated and automated processing system of the deoxyribonucleic acid sequence information of the present invention.

2 is a flowchart of a pipeline program used in the pipelined interworking method of the present invention.

3 is a flow chart for the pipeline program of 410 of FIG.

4 is a flow chart for the NCBI sequence database automatic mirroring program of 310 of FIG.

Figure 5 is the initial screen of the integrated and automated processing system of the deoxyribonucleic acid sequence information of the present invention.

6 is an input screen of a pipeline program for inputting user information and analysis project information.

7 is an input screen for selecting each process for the integration and automated processing of deoxyribonucleic acid sequence information.

8 is an input screen for setting user selections of programs used in each processing step.

9 is a status screen outputting the standard output contents and the progress rate during the integration and automated processing of deoxyribonucleic acid sequence information.

10 is a screen for selecting the base sequences to be used or excluded in the analysis according to the results after repeat masking (repeat masking) during the integration and automated processing of deoxyribonucleic acid nucleotide sequence information.

11 is a user selection input screen for processing deoxyribonucleic acid sequences and storing the results in a database after the similarity analysis.

12 is a comprehensive result output screen for querying and showing the processing result, similarity analysis result and intermediate processing result of the nucleotide sequence information stored in the database.

FIG. 13 is a screen for outputting a result of labeling a low quality region and a vector sequence among base sequence information stored in a database, and a base sequence of a high quality region from which these are removed. FIG.

14 is a screen for outputting a result of similarity analysis of nucleotide sequences stored in a database.

15 is a screen for inquiring detailed information of similar genes obtained from similarity analysis results of nucleotide sequences stored in a database using the Entrez program of the National Center for Biotechnology Information (NCBI) of the United States and outputting the results.

16 is a screen for outputting clustering results stored in a database.

FIG. 17 is a screen for outputting multiple sequence alignment analysis results between parent and child sequences constituting a cluster from clustering results stored in a database. FIG.

18 is a screen for organizing and outputting statistics on clustering results for each project which is an analysis unit.

* Brief description of symbols for the main parts of the drawing *

10: raw data 100: base sequence processing unit

110,130,150,170,190,210,410: pipeline processing unit

120: base calling 140: vector masking

160: repeat masking 180: clustering

195: Contig Assembly 200: Similarity Analysis

220: BLAST230: Regional Database

300: database mirroring unit 310: automatic mirroring unit

320: NCBI sequence database 400: database portion

420: database storage unit 430: database

440: search unit 450: visualization report

In order to achieve the above object, the method of the present invention inputs base sequence source information, and integrates processes such as base calling, vector masking, repeat masking, clustering, and contiguous assembly by pipeline method. Automated processing, and analyzing the similarity of the processed nucleotide sequence information to the existing registered genetic information, and creating and visualizing the processed nucleotide sequence information and similarity analysis results in a database.

In the present invention, a pipelined program interworking technique has been developed to integrate complex processing of deoxyribonucleic acid sequence information into an automated method, and to create a graphical user environment to apply the user's options for each processing step. To facilitate.

In addition, in the present invention, by using the present deoxyribonucleic acid sequence information processing system by producing a program that automatically mirrors (sequentially automatic mirroring) the sequence database manufactured and managed by the US NCBI, and the existing genetic information stored in the database The comparative search can be processed in this system to prevent information exposure problem.

In addition, by making a dedicated database that stores the results of comparison search with the existing genetic information stored in the sequence database to be useful for future additional purposes.

Similarity analysis in the present invention is performed by the BLAST algorithm.

In the present invention, for the base calling process, processes such as storage location information, copy location information, storage location information of intermediate result files, storage location information of result files, directory generation, and file copying are performed in a pipelined manner. Is performed.

In the present invention, the base calling files are integrated in the base calling process for the vector masking process, and user input is selected.

In the present invention, a user selection setting, a low quality region or a nucleotide sequence of a vector are removed for the repeat masking process.

In the present invention, the input information is processed to match the input format of the clustering processing program for the clustering process, and the input information is processed to match the input format of the contig assembly processing program for the contig assembly processing.

Hereinafter, the present invention will be described in detail with reference to the accompanying drawings.

Figure 1 shows the processing flow of the deoxyribonucleic acid sequence information integration and automated processing system of the present invention.

Referring to FIG. 1, the system of the present invention includes a base sequence processor 100, a similarity analyzer 200, a sequence database mirroring unit 300, and a database unit 400.

The nucleotide sequence processing unit 100 inputs the nucleotide sequence raw data 10. The nucleotide sequence data 10 is a chromatogram file obtained from a sequencing analyzer.

The sequencing processor 100 performs a series of processes such as base calling 120, vector masking 140, repeat masking 160, clustering 180, and contig assembly 195. In the step is configured to go through the pipeline processing (110, 130, 150, 170, 190) respectively.

For the base calling 120, chromatogram files 10 must be processed to match the data input method of the base calling program. This process is for inputting location information where chromatogram files are stored, inputting location information (directory or storage path) to be copied to process chromatogram files, intermediate result files generated during processing, and for future use after processing. It includes inputting location information to save result files to be kept, creating directory, copying files, etc. These functions are handled by pipeline program 110.

The base calling process 120 refers to a process of obtaining a base sequence consisting of A, T, G, and C letters indicating deoxyribonucleic acid base from a chromatogram. A program for this has been developed and used. The base calling process also outputs information that distinguishes the high and low quality regions of the analyzed base sequence. Depending on the sequencing analyzer, base calling may already be performed. In this case, base calling is not necessary.

The process of tying the base calling files of the base calling sequence into one and inputting a user option are processed in the pipeline processing 130 to perform the next vector masking. The vector masking 140 may include gene information of a vector used for gene amplification in the source data of the sequencing information obtained from the sequencing analyzer, and the base calling may be performed because the vector uses a known type of sequencing. The base sequence of a vector can be compared and displayed from the completed base sequence.

Subsequently, in order to perform the repeat masking operation, the input data needs to be processed in accordance with the input format of the program, and appropriate user options must be set. In addition, in order to reduce unnecessary processing, the pipeline processing 150 is performed to remove the low quality region, the base sequence of the vector, and the like, which are labeled by the base calling ring 120 and the vector masking 140. Repeat masking 160 refers to displaying a repeat unit existing in the base sequence.

In the pipeline processing 170, input data must be processed according to a user's desired result and input form of a program, and a task of setting an appropriate user option is performed. The clustering 180 performs grouping processing of short fragments having a common sequence of the same region into clusters. The base sequence that can best represent the cluster in one cluster is called a parent sequence, and the remaining sequences are called child sequences.

In the pipeline processing 190, in order to apply the Contig Assembly 195 program, it is necessary to process input data according to the input format of the program and according to the user's purpose, and to set appropriate user options. Perform The contig assembly 195 refers to a process of acquiring longer contig information by synthesizing information of shorter length sequences.

The base sequence processed through the process shown in the nucleotide sequence processor 100 is provided to the similarity analyzer 200. The similarity analysis unit 200 analyzes the similarity with existing registered genetic information stored in the NCBI sequence database (200).

The similarity analysis unit 200 processes the base sequence input through the pipeline processing 210 into an appropriate form in order to use the similarity analysis program, selects a user option, and then NCBI sequence to maintain processing speed and security. The local database 230 mirrored the database is used, and the similarity analysis uses a program employing the BLAST algorithm 220.

For similarity analysis, it is desirable to keep the regional sequence database 320 up-to-date at all times, which requires regular data updates.

The NCBI sequence database 320 includes an automatic mirroring unit 310 that implements a program 300 for automatically mirroring the NCBI sequence database in accordance with this cycle since the added data are updated at monthly intervals. Users can always access the latest data without additional effort and can prevent the leakage of information that may be subject to intellectual property rights.

The analyzed base sequence information and the intermediate result file generated during the analysis are stored in the database 400 for future reference. In order to analyze the files generated in each processing step and to store them in the database 400, the process goes through a pipeline processing unit of 410 which is a process of generating a data record suitable for the database structure.

The generated records are stored in a dedicated database 430 using a storage program. Materials stored in the database 430 may be searched through the search unit 440 using an appropriate keyword, and the searched results may be written in an appropriate form, for example, an HTML document 450, to be effectively displayed to the user. Output through The output form and method can be implemented in various ways, but the form of a web document is suitable for linking related data to each other and effectively delivering it to a user according to the relationship between the output data.

When operating a user environment of a database in the form of a web document, the database can be searched from a local or remote computer connected to a network.

Each of the pipeline processing units 110, 130, 150, 170, 190, and 210 processes data in accordance with the flowchart of FIG. 2.

Referring to FIG. 2, it is checked whether the unit analysis is performed by receiving data from a previous unit analysis program (510). If the unit analysis is not performed in step 510, the next pipeline program is executed (504). If the unit analysis is performed, the unit analysis program option is output (506). After setting the option, the user checks whether there is an option to analyze in order to extract option values (508), or executes the next unit analysis program (510).

In step 508, if there is an option to be analyzed, it is checked whether an option is selected (512), or step 508 is performed. If the option is selected, it is checked if it is a file / directory option (514), and if it is a file (516). If it is a file option, a file is selected (518), or a directory is selected (520).

After the file or directory is selected, the file is processed (522), and it is checked if the selected file and directory exists inside the analysis directory (524). Otherwise, copy to the analysis directory (526), if present, and if it is not a file or directory option in step 514, the option value is stored in the transfer variable (528), and step 508 is performed. In step 522, the base calling unit analysis is not applicable. In the vector masking unit analysis, the input file is integrated into a single file. In addition, in the case of repeat masking unit analysis, displayed error and low quality region data are removed, and in clustering unit analysis, data is selected according to the labeled repeating unit amount. Data for each cluster is reconstructed in unit analysis of contig assembly, and data for similarity analysis is selected in similarity analysis.

Referring to FIG. 3, the pipeline processing unit 410 of the database unit 400 checks whether to store data provided from the BLAST 220 in the database (411) or performs step 440.

When storing the data, the database stored data is extracted from the similarity analysis result (412). Then, it is checked whether the option remains (413), or if the database storage 420 is performed, and if it is the database stored data (414). If the data storage data, the database storage data is extracted from the option value (415) and step 413 is performed.

Referring to FIG. 4, the automatic mirroring process 310 accesses the mirroring server (311) and inquires and analyzes the database update time (312). It is checked whether the database update time is greater than the mirroring time (313), or otherwise 110 processing is performed.

If it is large in step 313, the database file is downloaded (314) and disconnected from the mirroring server (315). Next, the downloaded database file is decompressed (316) and the mirroring time is stored (317).

5 shows an initial screen of a deoxyribonucleic acid nucleotide sequence processing program according to the present invention. When the desired analysis process is selected on the initial screen, an input screen of a pipeline program for inputting user information and analysis project information of FIG. 6 appears. In the screen of FIG. 6, a researcher name, a project code, a project description, and the like are input. Subsequently, each of the processes for integrating and automating the deoxyribonucleic acid sequence information in FIG. 7 is selected.

On the screen of FIG. 8, user selections of programs used in each processing step are set.

The screen of FIG. 9 displays the standard output content and the progress rate during deoxyribonucleic acid sequence integration and automated processing. The screen of FIG. 10 illustrates a process of selecting base sequences to be used or excluded from analysis according to the results after repeat masking during the integration and automated processing of deoxyribonucleic acid nucleotide sequence information.

11 shows a user selection input screen for processing a deoxyribonucleic acid sequence, and storing the result in a database after the similarity analysis is completed. The screen of FIG. 12 shows a result of inquiring a processing result, a similarity analysis result, and an intermediate processing result of the nucleotide sequence information stored in the database and showing the result to the user.

The screen of FIG. 13 shows the results of labeling the low quality region and the vector sequence among the nucleotide sequence information stored in the database, and shows the nucleotide sequence of the high quality region from which they are removed. The screen of FIG. 14 shows a result of similarity analysis of nucleotide sequences stored in a database. In the screen of FIG. 15, detailed information of similar genes obtained from similarity analysis results of nucleotide sequences stored in a database is inquired using NCBI's Entrez program and the result data is displayed. The screen of FIG. 16 shows a clustering result stored in a database, and the screen of FIG. 17 shows a multisequence alignment analysis result between parent and child sequences constituting a cluster from the clustering result stored in a database.

In the screen of FIG. 18, statistical values of clustering sequencing information for each project as an analysis unit are displayed.

If processing the sequencing information using the integrated sequencing and automated processing method and system according to the present invention may be subject to intellectual property rights that may occur when processing the sequencing information by other existing professional processing institutions It can solve the problem of information exposure and minimize the cost and waiting time of processing request.

Multi-stage data processing is simplified with automated integrated processing, and the application of the graphical user environment is applied step by step, compared to the existing methods that are complicated and difficult to use even if they are used by those who have the ability to process their own. Easy to use options can greatly increase processing efficiency.

In addition, since the processing results are immediately stored in the database, and the data can be easily retrieved and reused later, it will greatly contribute to improving work efficiency in the fields related to the processing and utilization of genetic information.

Claims (7)

In the processing of the sequence information obtained from the deoxyribonucleic acid sequencing analyzer, the deoxyribonucleic acid sequencing of the deoxyribonucleic acid sequence information comprising a multi-step integration process and an automated processing method and an automatic mirroring method of an NCBI sequence database using a mirroring program. Integration and automated processing. The method of claim 1, wherein the processing of the sequencing information obtained from the deoxyribonucleic acid sequencing analyzer comprises: from base calling to vector and host sequence masking, repeat masking, clustering, contiguous assembly, similarity analysis, storage and query in a database. Method for integrating and automating deoxyribonucleic acid sequence information, characterized in that. The method according to claim 2, wherein the deoxyribonucleic acid sequence information is integrated and automated. 4. The method according to claim 3, wherein said pipeline programs input and process user options of program-by-process programs using a graphical user environment. According to claim 1, Integration and automated processing of deoxyribonucleic acid nucleotide sequence information, characterized in that for periodically analyzing the similarity of the base sequence data of the sequence database of the NCBI mirrored to the regional database automatically updated using a program Way. The method for integrating and automating deoxyribonucleic acid sequence information according to claim 2, wherein the sequence processing result, the similarity analysis result, and intermediate results during the processing are immediately stored and inquired by interworking with a database. The method of claim 6, wherein the data stored in the database are linked to each other in a web document format and linked to each other to output the deoxyribonucleic acid sequence information.