CN115240769B - Probe design interaction system based on Internet - Google Patents
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- G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
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Abstract
The invention provides an internet-based probe design interaction system which comprises a probe design cloud platform user end, a probe design cloud platform manager end and a probe design cloud platform server processing end, wherein the probe design cloud platform manager end is used for managing and maintaining user information, the probe design cloud platform server end is used for calculating and storing results, an annotating module is used for annotating a design area and a database selected by a user, the probe design system provides detailed parameters for the user to select, provides a result report for downloading, provides display data for checking, checks the coverage of the design area, and meets user humanized online design experience, personalized scheme requirements on the probe design and probe design requirements for pursuing high quality.
Description
Technical Field
The invention relates to the technical field of Internet, in particular to an Internet-based probe design interaction system.
Background
The advent of second generation sequencing technology (Next-Generation Sequencing, NGS) has pushed life sciences into the high throughput sequencing era. Although the throughput of sequencing by the second generation sequencing technology is higher and lower, the huge amount of data of whole genome sequencing of hundreds of samples cannot make the sequencing become a viable option for most genetic laboratories and complex diseases, so that the target sequence targeted capture sequencing has the potential of greatly exerting the second generation sequencing technology.
Target sequence targeted capture sequencing is a research strategy for customizing a specific probe to a genomic region of interest, hybridizing with a genomic DNA fragment, capturing the fragment of the target genomic region, amplifying and enriching by PCR, and sequencing by using a second generation sequencing technology. The target sequence targeted capture sequencing not only utilizes the high flux of the sequencing technology of the second generation sequencing technology, but also reduces the cost of sequencing the target sequence, and simultaneously reduces the analysis difficulty of mass data generated after sequencing, thereby being a hot spot technology in the current genomics research.
In addition, the quality of the probe design is the basis for determining the quality of hybridization capture in target capture sequencing of a target sequence. In designing probes for genomic target regions, a number of factors need to be considered: 1) The risk of probe off-target is reduced as much as possible, and off-target probes can capture non-target areas, so that the coverage of the target areas is reduced or uncovered; 2) When designing a probe for a target region with low GC content, the probe density is properly adjusted, the GC content laterally reflects the number of hydrogen bonds combined by two chains, and the unstable chain combination is caused by the low number of hydrogen bonds; 3) A suitable probe length; 4) The target region contains as little repetitive sequences as possible, and the like.
There are few open probe design platforms in China, and there are certain limitations in function, such as: only DNA probes can be designed, but RNA and methylation probes cannot be designed; when designing, the flexibility of design parameters is low, and the parameter description is fuzzy; the actual capture of the probe is unknown, etc.
Disclosure of Invention
The invention aims to provide the probe design interaction system based on the Internet on the basis of breaking through the limitation, and the probe design interaction system can provide user humanized online design experience and high-quality probe design results. In order to achieve the technical effects, the technical scheme of the invention is as follows:
an internet-based probe design interaction system for providing online submission of design orders by a user, comprising: the probe design cloud platform user end includes: the probe system provides probe design parameters for users to select, the users submit design tasks after filling in the design parameters and inputting the design parameters, the submitted contents are connected with a probe design cloud platform server processing end through a wireless or wired communication protocol to calculate and generate a design result, and the design result is fed back to the probe design cloud platform user end; and a DNA design module for providing the user named probe design name, selecting a reference genome, and selecting whether to use fasta format files as input files; the probe design cloud platform administrator end includes: the information management system is used for managing the basic information of the user and adjusting and modifying the grade and the user authority of the registered user; the order management system is used for managing the design order and converting the design order into an order according to the selection of the user; the message prompt system is used for notifying the user of the message; the data maintenance system is used for adding, modifying and maintaining the help center data of the help center displayed on the probe design cloud platform user side; the probe design cloud platform server processing end includes: the information transfer module is used for receiving the design order from the probe design cloud platform user side; the calculation module receives the design order from the information transmission module, reads design parameters in the design order, performs probe design processing, and sends the design result to the information transmission module after the design is completed; and a storage module storing the design result from the calculation module; and after the calculation module finishes calculation, feeding back the design result to the probe design cloud platform user end and the probe design cloud platform manager end.
Preferably, the DNA design module of the probe design cloud platform user terminal performs synonym check on the name of the gene input by the user, and checks whether the gene does not include a coding region but only selects the coding region to design a probe, and checks whether the gene exists; performing region size check on the bed file input by the user according to the selected genome version; and checking whether the SNP, ensembl ID, transcript and CCDS ID input by the user exist.
Preferably, the DNA design module at the user end of the probe design cloud platform calculates the sizes of the design areas respectively to obtain the total design area size, if the total design area size does not exceed a set design area threshold, the design is performed, and if the total design area size exceeds the set design area threshold, the user is prompted to redesign.
Preferably, the DNA design module at the user end of the probe design cloud platform further includes a data verification module and a database, the database selects a probe set for NAD verification, the design area selects the coding area, the probe density selects 1x probes, after clicking to enter design details, a data verification button is provided, after clicking, loading data is selected, and coverage condition of the demonstration data in the design area is checked.
Preferably, the probe design cloud platform user side further includes a methylation design module, the methylation design module provides the user to name the probe design name and select the reference genome, the methylation design module further provides the user to name the probe design panel name in a custom manner, after selecting different genome versions, the user only selects a file with a non-fasta format as the input file, a validated probe library database is selected, 1x probes or 2x probes are designed for a gene coding region, a coding region and an upstream and a downstream non-coding region, the database which is not validated is also selected, the 1x probes or the 2x probes are designed after removing all dangerous regions, high-risk regions, or the 1x probes or the 2x probes are designed after removing all dangerous regions, high-risk regions, such as bed files, SNPs, enmbl IDs, transcripts, CCDS IDs, other than genes.
Preferably, the methylation design module performs synonym check on the name of the gene input by the user, checks whether the gene does not contain a coding region but only selects a coding region design probe, and checks whether the gene exists, the methylation design module performs region size check on the bed file input by the user according to the selected genome version, the methylation design module checks whether the SNP, the Ensembl ID, the transcript and the CCDS ID input by the user exist, and the methylation design module respectively calculates the design region sizes to obtain the total design region size, performs design if the total design region size does not exceed a set design region threshold, and prompts the user to redesign if the total design region size exceeds the set design region threshold.
Preferably, the probe design cloud platform user terminal further includes an RNA design module, where the RNA design module provides the user to name the probe design panel name by user definition, and then selects DNA-RNA co-hybridization, designs the 1x probe or the 2x probe for the gene coding region, the coding region, and the upstream non-coding region, and then selects non-DNA-RNA co-hybridization after the user to name the probe design panel name by user definition, and then uploads fasta files, transcripts, and gene selection to design the 1x probe or the 2x probe.
Preferably, the probe design cloud platform user terminal further comprises a microbial genome design module, and the microbial genome design module only supports manual design.
Preferably, the DNA design module and the methylation design module further include an annotation module, wherein the annotation module is used for annotating the design area and the database selected by the user, displaying annotation results to the user for reference in a table form, and providing the annotation result compression package for the user to download and then to browse locally.
Preferably, the probe design cloud platform user end further comprises a bill making system, the bill making system comprises an information transmission module and a result downloading and displaying module, the information transmission module is unidirectional, a technician and a user communicate with each other, and then remarks are added to a bill making order at the probe design cloud platform manager end, or bill making progress is fed back to the user, meanwhile, the probe design cloud platform user end synchronously remarks and progress information, after the probe is synthesized, quality inspection is qualified, the technician sends the bill making result to the probe design cloud platform user end through the probe design cloud platform manager end, the result downloading and displaying module clicks a bill making button in a bill making list of the probe design cloud platform user end, a bill making detail displaying page is jumped, basic information and design parameters of a bill making design task are converted into a bill making detail displaying page, the design result is summarized, and updating bill making progress is implemented in the remark. For the completed task of ordering, a download button in the order list of the probe design cloud platform user side can be clicked to download a download single-fruit compression package, for the completed task of designing, a download button in the design list of the probe design cloud platform user side can be clicked to download a design result compression package, the design result compression package contains a report PDF file which informs the user of the coverage condition of the designed probe to the total design area and the coverage condition of each designed probe in the design area, the design task in the design list of the probe design cloud platform user side is clicked, the design detail display page is jumped, and the basic information of the design task, the design parameters during design and the design area display are displayed in the design detail display
Drawings
The accompanying drawings, which are included to provide a further understanding of the invention and are incorporated in and constitute a part of this specification, illustrate embodiments of the invention and together with the description serve to explain the invention. In the drawings:
fig. 1 is a schematic diagram of an internet-based probe design interaction system according to an embodiment of the present invention.
Fig. 2 is a schematic diagram of a platform main page of an internet-based probe design interaction system according to an embodiment of the present invention.
FIG. 3 is a schematic diagram of a probe design interactive system DNA panel based on the Internet according to an embodiment of the invention.
Fig. 4 is a schematic diagram of a DNA panel design input of an internet-based probe design interaction system according to an embodiment of the present invention.
FIG. 5 is a schematic diagram of a DNA panel design input verification of an Internet-based probe design interaction system according to an embodiment of the present invention.
FIG. 6 is a schematic diagram of a DNA panel design input verification of an Internet-based probe design interaction system according to an embodiment of the present invention.
FIG. 7 is a diagram of an Internet-based probe design interactive system design list and the following list of representations of intents according to an embodiment of the present invention.
FIG. 8A is a schematic diagram of a task of designing a probe design interactive system for Internet according to an embodiment of the present invention.
FIG. 8B is a schematic diagram of a genome browser of a probe design interactive system for Internet according to an embodiment of the present invention.
FIG. 8C is a schematic diagram of coverage of a probe design interactive system design area on the Internet according to an embodiment of the invention.
FIG. 9 is a schematic diagram of a customized design of a probe design interactive system for Internet according to an embodiment of the present invention.
FIG. 10 is a schematic diagram of a customized design of a probe design interactive system for Internet according to an embodiment of the present invention.
FIG. 11 is a schematic diagram of a customized design of a probe design interactive system for Internet according to another embodiment of the present invention.
FIG. 12 is a schematic diagram of an annotation page of a probe design interactive system for Internet according to another embodiment of the present invention.
FIG. 13 is a diagram of a gene details page of an interactive system for probe design on the Internet according to another embodiment of the present invention.
100-probe design interaction system
110-probe design cloud platform user
1101-probe system
1102-DNA design Module
11022-data verification module
11042 database
1103-help centre
1104-methylation design module
1105-RNA design module
1106-microbial genome design module
1107-ordering system
11072 information transfer module
11074-results download and display module
130-probe design cloud platform manager end
131-information management system
132-order management system
133-message alert system
134-data maintenance system
150-probe design cloud platform server processing end
151-information transfer module
152-computing module
153-storage module
T-technician
U-user
O 1 -design order
O 2 -placing an order
D n Help centre data
Detailed Description
The present invention will be described in further detail with reference to the drawings and examples, in order to make the objects, technical solutions and advantages of the present invention more apparent. It should be understood that the specific embodiments described herein are for purposes of illustration only and are not intended to limit the scope of the invention. All other embodiments, which can be made by those skilled in the art based on the embodiments of the invention without making any inventive effort, are intended to be within the scope of the invention.
The present invention provides an internet-based probe design interaction system 100 that provides for user U to submit design orders online. The internet-based probe design interaction system 100 includes: the probe design cloud platform user end 110, the probe design cloud platform manager end 130 and the probe design cloud platform server processing end 150. The probe design cloud platform user terminal 110 includes: probe system 1101, DNA design module 1102, help center 1103, methylation design module 1104, RNA design module 1105, microbial genome design module 1106, and ordering system 1107.
The probe system 1101 provides probe design parameters for the user U to select, the user U submits design tasks after filling in the design parameters and inputting, the submitted content is connected to the probe design cloud platform server processing end 150 through a wireless or wired communication protocol to calculate and generate a design result, and the design result is fed back to the probe design cloud platform user end 110.
The DNA design module 1102 is used to provide the user U with a name for the probe design, to select a reference genome, and to select whether to use fasta format files as input files.
The probe design cloud platform administrator terminal 130 includes: an information management system 131, an order management system 132, a message prompt system 133, and a data maintenance system 134. Information management system131 is used for managing the basic information of the user U, and adjusting and modifying the registered user level and the user authority. Order management system 132 is used to manage design order O 1 And according to the selection of the user U, the design order O 1 To order O 2 . The message prompt system 133 is used for notifying the user U of the message. The data maintenance system 134 is used for providing the help center data D of the help center 1103 displayed on the probe design cloud platform user terminal 110 h And performing addition and modification maintenance.
The probe design cloud platform server processing terminal 150 includes: an information transfer module 151, a calculation module 152, and a storage module 153. The information transfer module 151 is configured to receive a design order O from the probe design cloud platform client 110 1 . The calculation module 152 receives the design order O from the information delivery module 151 1 Reading the design order O 1 In the design parameters, probe design processing is carried out, and the design result O is obtained after the design is completed 2 To the information delivery module 151. The storage module 153 stores the design result O from the calculation module 152 2 And storing. After the calculation module 152 completes the calculation, the design result is fed back to the probe design cloud platform user terminal 10 and the probe design cloud platform manager terminal 130.
The DNA design module 1102 of the probe design cloud platform user terminal 110 performs synonym check on the name of the gene input by the user U, check whether the gene does not include a coding region but only selects a coding region to design a probe, and check program to check whether the gene exists.
And checking the region size of the bed file input by the user U according to the selected genome version. And checking whether SNP, ensembl ID, transcript, CCDS ID input by the user U exist. The DNA design module 1102 counts the design area sizes, respectively, to obtain the total design area size. If the total design area size does not exceed the set design area threshold, the design is performed. If the total design area size exceeds the set design area threshold, the user is prompted to redesign.
The DNA design module 1102 includes a data verification module 11022 and a database 11024. When database 11024 selects the NAD-verified probe set, its design region will select the coding region and probe density will select 1 probe. After clicking to enter the design details, a data verification button is arranged, after clicking, loading data is selected, and the coverage condition of the demonstration data in the design area is checked.
The data display flow of the probe design interaction system based on the Internet comprises the steps that when a user U uses the probe design interaction system 100 based on the Internet, the user U logs in a platform at first, two login modes are adopted, one login mode is account number and password login, and the other login mode is WeChat code scanning login. The precondition of the WeChat code login is to pay attention to WeChat public numbers of the probe design platform. Referring to fig. 2, fig. 2 is a schematic diagram of a platform main page of an internet-based probe design interaction system according to an embodiment of the present invention. The main page of the platform clicks on the DNA panel and enters the design of the DNA panel.
Referring to fig. 3, fig. 3 is a schematic diagram of a DNA panel of an internet-based probe design interaction system according to an embodiment of the present invention. Clicking the DNA Panel on the main page of the platform, entering the design of the DNA Panel, inputting 5 parameters of fasta, database, region, risk and probe density, and clicking the next step after filling the parameters according to the following diagram. Referring to fig. 4, fig. 4 is a schematic diagram illustrating a DNA panel design input of an internet-based probe design interaction system according to an embodiment of the present invention. The input boxes are filled with "TP53, TEST, TERC, A B" (Gene name), and the next step is clicked. Referring to fig. 5, fig. 5 is a schematic diagram illustrating a DNA panel design input verification of an internet-based probe design interaction system according to an embodiment of the present invention. And (3) carrying out three checks of synonym detection, non-coding genes and input of corresponding information which is not found on the input of the previous step, checking the genes which need to be confirmed and designed, and clicking the next step. Referring to fig. 6, fig. 6 is a schematic diagram illustrating a DNA panel design input verification of an internet-based probe design interaction system according to an embodiment of the present invention. And (3) counting the number of the designed regions and the base length in the region of the gene confirmed in the previous step, and clicking to confirm the designed regions. Referring to fig. 7, fig. 7 shows a design list and the following list of the interactive system design for the probe design based on the internet according to the embodiment of the present invention. The submitted design task starts to design, and when the design is completed, the WeChat and the mailbox receive prompts at the same time, and click is carried out to enter design details. Referring to fig. 8A, 8B and 8C, fig. 8A is a schematic diagram illustrating a task of designing an interactive system for designing a probe on the internet according to an embodiment of the invention. FIG. 8B is a schematic diagram of a genome browser of a probe design interactive system for Internet according to an embodiment of the present invention. FIG. 8C is a schematic diagram illustrating coverage of a design area of a probe design interaction system for Internet according to an embodiment of the present invention. Clicking on the data in the design task page validates (as shown in FIG. 8A) and pops up the genome browser as shown in FIG. 8B. And (3) checking the file to be checked on the left, selecting a chromosome region or inputting a gene name, and checking the coverage condition of the display data in the design region, as shown in fig. 8C, so as to complete the data display flow.
The probe design cloud platform user terminal 110 includes a methylation design module 1104. The methylation design module 1104 provides a user U with a named probe design name and selects the reference genome, the methylation design module 1104 provides a user U with a custom named probe design panel name, and after selecting different genome versions, the user U only selects a file with a non-fasta format as an input file, selects a verified probe library database, designs a 1x probe or a 2x probe for a gene coding region, a coding region and an upstream non-coding region, and also selects the database which is not verified, designs the 1x probe or the 2x probe after removing all dangerous regions, high-risk regions and upstream non-coding regions of the gene coding region, the coding region and the upstream non-coding region, or removes all dangerous regions for bed files, SNP, ensembl IDs, transcripts and CCDS IDs except genes, and designs the 1x probe or the 2x probe after removing the high-risk regions.
The probe design cloud platform user terminal 110 includes a methylation design module 1104. Methylation design module 1104 performs synonym checking for the name of the gene entered by user U, checking for whether the gene does not contain coding regions, but only selects coding region design probes, and checking for the presence of the gene. The methylation design module 1104 performs region size checking on the bed file input by the user U according to the selected genome version. In addition, the methylation design module 1104 checks whether the SNP, the Ensembl ID, the transcript, and the CCDS ID entered by the user U are present. The methylation design module 1104 calculates the design region size, respectively, to obtain the total design region size. If the total design area size does not exceed the set design area threshold, the design is performed. If the total design area size exceeds the set design area threshold, the user U is prompted to redesign.
The DNA design module 1102 includes a data verification module 11022 and a database 11024. Database 11024 selects the NAD verified probe set, the design area selects the coding region, the probe density selects 1x probes, after clicking into design details, a data verification button is provided, after clicking, loading data is selected, and the coverage condition of demonstration data in the design area is checked.
Methylation design module 1104 provides user U with the name of the probe design, and selects a reference genome. The methylation design module 1104 further provides the custom named probe design panel name, and provides the user to select only a non-fasta format file as the input file, select a validated probe library database, design 1x probes or 2x probes for a gene coding region, a coding region and an upstream non-coding region, and also select an unverified database, design the 1x probes or the 2x probes after removing all dangerous regions, high-risk regions, or design the 1x probes or the 2x probes after removing all dangerous regions for the gene coding region, the coding region and the upstream non-coding region, or remove all dangerous regions for bed files, SNPs, ensembl IDs, transcripts, CCDS IDs other than genes.
The methylation design module 1104 performs synonym check on the name of the gene input by the user U, check whether the gene does not contain a coding region but only selects a coding region design probe, and check program whether the gene exists, and the methylation design module performs region size check on the bed file input by the user according to the selected genome version. The methylation plan module 1104 checks for the presence of SNPs, ensembl IDs, transcripts, and CCDS IDs entered by the user U. The methylation design module 1104 calculates the design area size to obtain the total design area size, and designs if the total design area size does not exceed the set design area threshold. If the total design area size exceeds the set design area threshold, prompting the user to redesign.
The methylation design module 1104 has the following features:
1. user U may autonomously name the probe design name and select the reference genome.
2. After the user U has custom named probe design interface names and selected different genome versions, the user U can only select files in a non-fasta format as input files. The library database of validated probes may then be selected and probes for the 1x probe or 2x probe may be designed for the coding region, coding region and upstream and downstream non-coding regions of the gene.
3. The database can also be selected from unverified databases, and 1x probes or 2x probes are designed after all dangerous areas are removed from the coding area, the coding area and the upstream and downstream non-coding areas of the genes, high-risk areas are removed, or 1x probes or 2x probes are designed after all dangerous areas are removed from bed files, SNP, ensembl IDs, transcripts and CCDS IDs except the genes.
The methylation design module 1104 has the following subsequent inspection steps: 1, a synonym check is performed on the name of the gene input by the user U, a check is performed on whether the gene does not contain a coding region but only a coding region design probe is selected, and whether there is a check.
2. And checking the region size of the bed file input by the user U according to the selected genome version.
3. Check whether SNP, ensembl ID, transcript, CCDS ID entered by user U are present.
4. And respectively counting the sizes of the areas of the checked input to obtain the total design area size. If the total design area size does not exceed the set design area threshold, the design is given. If the total design area size does not exceed the set design area threshold, the user is prompted to redesign.
The probe design cloud platform user terminal 110 includes an RNA design module 1105.RNA design module 1105 provides user U user definition naming probe design panel name, then selects DNA-RNA co-hybridization, designs 1x probe or 2x probe for gene coding region, coding region and upstream and downstream non-coding region, and user U definition naming said probe design panel name. Alternatively, non-DNA-RNA co-hybridization may be used, with fasta files, transcripts, gene selection to design 1x probes or 2x probes. The RNA design module 1105 is characterized in that:
1. after the user U designs interface names by defining and naming probes, DNA-RNA co-hybridization can be selected, and 1x or 2x probes are designed for the coding region/coding region and upstream and downstream non-coding regions of the gene;
2. after the user U designs the interface name by self-defining and naming the probe, the non-DNA-RNA co-hybridization can be selected, and the fasta file, the transcript and the gene can be uploaded to select and design the 1x probe or the 2x probe.
The probe design cloud platform user side 110 includes a microbial genome design module 1106 that supports only manual design.
The invention has the advantages that: the probe design cloud platform client 110 includes four probe design modules: DNA design module 1102, methylation design module 1104, RNA design module 1105, and microbial genome design module 1106. Wherein, the DNA design module 1102, the methylation design module 1104, and the RNA design module 1105 all support online designs that all have detailed parameters for the user U to select. In addition, a probe design result report can be provided for a user U to check, so that the personalized scheme requirement of the user on the probe design is met. The microbial genome design module only supports manual design, and in addition, the probe design cloud platform user terminal 110 simultaneously provides commercialized interfaces with various specifications for users to select.
The DNA design module 1102 of the probe design cloud platform client 110 has the following features:
1. user U may autonomously name the probe design name, select the reference genome, and select whether to use fasta format files as input files.
2. When the input file is selected to be in fasta format, the probe may be directly selected to be designed according to the probe density of 1x probe or 2x probe.
3. When the input file selects a non-fasta format, a library of validated probes may be selected, and either 1x probes or 2x probes are designed for the coding region/region of the gene and upstream and downstream non-coding regions.
4. When the input file selects a non-fasta format, an unverified database can be selected, and a 1x probe or a 2x probe is designed after all dangerous areas are removed from a gene coding area/coding area or upstream and downstream non-coding areas, or a 1x probe or a 2x probe is designed after all dangerous areas are removed from bed files, SNP, ensembl IDs, transcripts and CCDS IDs except genes.
The DNA panel design module of the probe design cloud platform user terminal comprises the following subsequent checking steps:
1. the name of the gene inputted by the user U was checked for synonym, whether the gene contained no coding region but only the coding region was selected for designing the probe, and whether there was a check.
2. And checking the size of the region of the bed file input by the user according to the selected genome version.
3. Check whether SNP, ensembl ID, transcript, CCDS ID entered by user U are present.
4. Respectively counting the sizes of the areas to obtain the total design area size, and if the total design area size does not exceed the set design area threshold value, giving design; if the total design area size exceeds the set design area threshold, the user is prompted to redesign.
The DNA design module 1102 and the methylation design module 1104 include an annotation module 11042. The annotation module 11042 is configured to annotate a design region selected by the user U and the database 11024, annotate region genes, bed, SNPs, ensembl IDs, transcripts, CCDS IDs, unified categorizing genes and Reference SNPs selected by the user U, display annotation results in a table form to the user U for Reference, and provide an annotation result compression package for the user U to browse locally after downloading.
The invention discloses an internet-based probe design interaction system platform annotation display flow, which comprises the following steps of 1, clicking DNA Panel or Methylation Panel to conduct design (note is only conducted in the results of the DNA Panel and Methylation Panel, and no requirement is required on parameters in the design, as shown in fig. 9. Fig. 9 is a customized design schematic diagram of an internet-based probe design interaction system according to the embodiment of the invention. Further, please refer to fig. 10, clicking a task completed to enter design details, choosing an input item and a database to be annotated, clicking an annotation button to submit an annotation task, clicking a skip view after the annotation is completed, as shown in fig. 11, fig. 11 is a customized design schematic diagram of an internet-based probe design interaction system according to another embodiment of the invention, as shown in fig. 12, fig. 12 is a schematic diagram of an internet-based probe design interaction system according to another embodiment of the invention, pages are displayed with notes, and point annotation results can be downloaded in the annotation page, and the annotation page is clicked, and the annotation page is transformed with the details of the gene is shown in fig. 13.
The probe design cloud platform client 110 includes an order placement system 1107. The ordering system 1107 includes an information transfer module 11072 and a result download and presentation module 11074. The information transmission module 11072 is unidirectional, and after a technician T communicates with a user U, a remark is added to the order placing order at the probe design cloud platform manager 130, or the order placing progress is fed back to the user U, meanwhile, the probe design cloud platform user 110 synchronously remarks and progress information, after the probe is synthesized, quality inspection is qualified, and the technician T transmits the order placing result to the probe design cloud platform user 110 through the probe design cloud platform manager 130. The result downloading and displaying module 11074 clicks an order button in an order list of the order placing system 1107 of the probe design cloud platform user terminal 110 to generate an order placing order number, jumps to an order placing detail display page, displays basic information and design parameters of a design task converted into an order placing, and briefly summarizes design results, and implements update order placing progress in notes. And for the completed order task, clicking a download button in the order list of the probe design cloud platform user terminal to download the single-fruit compression package.
For the completed design task, a download button in the design list of the probe design cloud platform user terminal 110 may be clicked to download the design result compression package. The design result compression package contains a report PDF file, informs the user U of the coverage of the designed probe to the total design area and the coverage of each designed probe in each design area, clicks on the design task in the design list of the probe design cloud platform user terminal 110, jumps to the design detail display page, and displays the basic information of the design task, the design parameters during design and the design area.
The probe design interaction system based on the Internet breaks through the limitations of single design, low flexibility of design parameters, ambiguous description, ambiguous design results and the like of the existing open probe function, and meets the requirements of a user on humanized online design experience, personalized scheme for probe design and high-quality probe design pursuit.
The foregoing is merely an example of the invention and is not intended to limit the scope of the invention and the terms "comprises," "comprising," or any other variation thereof herein are intended to cover a non-exclusive inclusion, such that a process, function, or method comprising a list of elements does not include only those elements but may include other elements not expressly listed or inherent to such process, function, or method. All equivalent structures or equivalent flow changes made by the specification and the attached drawings of the invention or directly or indirectly applied to other related technical fields are included in the protection scope of the invention.
Claims (8)
1. An internet-based probe design interaction system for providing online submission of design orders by a user, comprising:
the probe design cloud platform user end includes:
the probe system provides probe design parameters for users to select, the users submit design tasks after filling in the design parameters and inputting the design parameters, the submitted contents are connected with a probe design cloud platform server processing end through a wireless or wired communication protocol to calculate and generate a design result, and the design result is fed back to the probe design cloud platform user end; the method comprises the steps of,
the DNA design module is used for providing the user named probe design name, selecting a reference genome and selecting whether a fasta format file is used as an input file;
the probe design cloud platform administrator end includes:
the information management system is used for managing the basic information of the user and adjusting and modifying the grade and the user authority of the registered user;
the order management system is used for managing the design order and converting the design order into an order according to the selection of the user;
the message prompt system is used for notifying the user of the message; the method comprises the steps of,
the data maintenance system is used for adding, modifying and maintaining the help center data of the help center displayed on the probe design cloud platform user side;
the probe design cloud platform server processing end includes:
the information transfer module is used for receiving the design order from the probe design cloud platform user side;
the calculation module receives the design order from the information transmission module, reads design parameters in the design order, performs probe design processing, and sends the design result to the information transmission module after the design is completed; the method comprises the steps of,
the storage module stores the design result from the calculation module;
and after the calculation module finishes calculation, feeding back the design result to the probe design cloud platform user end and the probe design cloud platform manager end.
2. The internet-based probe design interaction system according to claim 1, wherein the DNA design module of the probe design cloud platform user performs synonym check on the name of the gene input by the user, check whether the gene does not include a coding region but only selects the coding region design probe, and check program for checking whether the gene exists, performs region size check on the bed file input by the user according to the selected genome version, and checks whether the SNP, ensembl ID, transcript, CCDS ID input by the user exist.
3. The internet-based probe design interaction system according to claim 2, wherein the DNA design modules of the probe design cloud platform user terminal respectively count the design area sizes to obtain a total design area size, if the total design area size does not exceed a set design area threshold, the design is performed, and if the total design area size exceeds the set design area threshold, the user is prompted to redesign.
4. The internet-based probe design interaction system of claim 2, wherein the probe design cloud platform user side further comprises a methylation design module, wherein the methylation design module provides the user to name the probe design name and select the reference genome, the methylation design module further provides the user to custom name a probe design panel name, and after selecting different genome versions, provides the user to select only a non-fasta format file as the input file, selects a validated probe library database, designs a 1x probe or a 2x probe for a gene coding region, a coding region and an upstream non-coding region, the probe library database is the database selected to be unverified, designs the 1x probe or the 2x probe after removing all risk regions, high risk regions, or removes all risk regions except genes, and designs the 1x probe or the 2x probe after removing all risk regions, the high risk regions, and removing the bed file, SNP, ensembl ID, transcript, CCDS ID.
5. The internet-based probe design interaction system according to claim 4, wherein the probe design cloud platform user side further comprises an RNA design module, wherein the RNA design module provides the user to custom name the probe design panel name, then selects DNA-RNA co-hybridization, designs the 1x probe or the 2x probe for the gene coding region, the coding region and the upstream and downstream non-coding regions, and then selects non-DNA-RNA co-hybridization after custom naming the probe design panel name, and can upload fasta files, transcripts, and gene selection designs the 1x probe or the 2x probe.
6. The internet-based probe design interaction system of claim 4, wherein the probe design cloud platform user side further comprises a microbial genome design module, the microbial genome design module supporting only manual design.
7. The internet-based probe design interaction system of claim 4, wherein the DNA design module and the methylation design module further comprise an annotation module for annotating the user-selected design area and database and presenting annotation results in tabular form to the user for reference, while providing the annotation result compression package for local browsing after download by the user.
8. The internet-based probe design interaction system according to claim 3, wherein the probe design cloud platform user side further comprises a ordering system, the ordering system comprises an information transmission module and a result downloading and displaying module, the information transmission module is unidirectional, a technician and a user communicate with each other and then add remarks to an ordering order at the probe design cloud platform manager side, or feed back ordering progress to the user, and meanwhile the probe design cloud platform user side synchronously notes and progress information, quality inspection after probe synthesis is qualified, the technician transmits ordering results to the probe design cloud platform user side through the probe design cloud platform manager side, the result downloading and displaying module clicks an ordering button in an ordering list of the probe design cloud platform user side, the ordering detail displaying page is jumped, the ordering detail displaying is converted into basic information and design parameters of an ordering design task, and the design results are brief and updated in the remarks are summarized; for the completed task of ordering, a download button in the order list of the probe design cloud platform user side can be clicked to download a single-node compression package, for the completed task of designing, a download button in the design list of the probe design cloud platform user side can be clicked to download a design result compression package, the design result compression package contains a report PDF file which informs the user of the coverage condition of the designed probe to the total design area and the coverage condition of each designed probe in the design area, the design task in the design list of the probe design cloud platform user side is clicked, the design detail display page is jumped, and the basic information of the design task, the design parameters during design and the design area display are displayed in the design detail display.
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Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1426534A (en) * | 2000-01-25 | 2003-06-25 | 阿菲梅特里克斯公司 | Method, system and computer software for providing genomic web portal |
| CN103642909A (en) * | 2013-11-28 | 2014-03-19 | 中国热带农业科学院南亚热带作物研究所 | Chip detection method for pineapple gene expression |
| CN112662767A (en) * | 2020-11-25 | 2021-04-16 | 深圳华大基因股份有限公司 | Kit and probe for measuring genomic instability and application of kit and probe |
-
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Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN1426534A (en) * | 2000-01-25 | 2003-06-25 | 阿菲梅特里克斯公司 | Method, system and computer software for providing genomic web portal |
| CN103642909A (en) * | 2013-11-28 | 2014-03-19 | 中国热带农业科学院南亚热带作物研究所 | Chip detection method for pineapple gene expression |
| CN112662767A (en) * | 2020-11-25 | 2021-04-16 | 深圳华大基因股份有限公司 | Kit and probe for measuring genomic instability and application of kit and probe |
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