CN110010203A - A kind of Interactive Dynamic qtl analysis system and method based on biological cloud platform - Google Patents
A kind of Interactive Dynamic qtl analysis system and method based on biological cloud platform Download PDFInfo
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Abstract
The invention discloses a kind of Interactive Dynamic qtl analysis system and method based on biological cloud platform, the system comprises: interactive analysis display module, interactive molecule intelligent screening module and Interactive Dynamic qtl analysis module；Interactive analysis display module obtains the first processing data for being imported and being analyzed to phenotypic data；Interactive molecule intelligent screening module obtains second processing data for screening and filtering to be marked to genotype data；Interactive Dynamic qtl analysis module, for carrying out qtl analysis to the first processing data and second processing data.Present system integrated level is high, user-friendly, and phenotypic data, genotype data, qtl analysis can complete correlation analysis content with one-touch parameter setting batch, reduce analysis threshold, promote user experience.
Description
Technical field
The present invention relates to biological fields, more particularly to a kind of Interactive Dynamic qtl analysis system based on biological cloud platform
System and method.
Background technique
Quantitative trait locus (QTL, quantitative trait locus) refers to the gene of control quantitative character in base
Because of the position in group, the relationship of qtl analysis whole gene group DNA molecular marker and quantitative trait phenotypes value detects the presence of QTL
And QTL is located on genetic map, determine the genetic distance between genetic marker and QTL.Based on two generations sequencing high density heredity
Map simultaneously carries out QTL positioning and has become one of common method when preceding crop, poultry, aquatic products functional gene excavate.
Molecular labeling and high throughput sequencing technologies fast development have become the important tool of qtl analysis research, and lower machine is sequenced
Effect of the biology information technology of data in the huge molecular biology information that processing generates also becomes increasingly conspicuous.How life is utilized
Object information technology excavates valuable core information from mass data, it has also become the core problem of field scientific research personnel.It passes
The data output of system analysis of biological information result is shown as static concluding report, and data displaying is not easy to easily to parse and crucial
Data mining generally requires scientific research personnel and grasps analysis of biological information method to static state knot to obtain better research effect
Fruit is corrected, this process is time-consuming and laborious.Sequencing demands, which are continued to increase, is not easy to scientific research personnel's analysis phase with data analysis result
Contradiction, to overcome the problems, such as this, one-touch parameter modification and mobilism analysis report become the hot spot method solved the problems, such as.
Apply for content
In order to solve the above-mentioned technical problems, the present invention provides a kind of Interactive Dynamic QTL based on biological cloud platform points
Analysis system and method, level of integrated system is high, user-friendly, and phenotypic data, genotype data, qtl analysis can be with one
Keyed parameter setting batch completes correlation analysis content, reduces analysis threshold, promotes user experience.
In order to reach the object of the invention, the present invention provides a kind of Interactive Dynamic qtl analysis based on biological cloud platform
System, the system comprises: interactive analysis display module, interactive molecule intelligent screening module and Interactive Dynamic QTL points
Analyse module；
Interactive analysis display module obtains the first processing data for being imported and being analyzed to phenotypic data；
Interactive molecule intelligent screening module obtains second processing for screening and filtering to be marked to genotype data
Data；
Interactive Dynamic qtl analysis module, for carrying out qtl analysis to the first processing data and second processing data.
Optionally, phenotypic data is imported and is analyzed including one or more in following manner: to phenotypic data into
The one-touch Phenotype Distribution analysis of row and the analysis of one-touch phenotypic parameter；
Optionally, label screening filtering includes one or more in following manner: one-touch customized selected marker lacks
Mistake rate, one-touch customized selection minimum mark genetic distance and one-touch customized selection minimum mark physical distance；
Qtl analysis includes one or more in following manner: one-touch qtl analysis software selection, the choosing of one-touch mode
It selects, one-touch parameter selection, one-touch qtl analysis whole result are shown and the enrichment analysis of the function of the one-touch section QTL gene；
Wherein parameter specifically includes: threshold value, LOD confidence interval
In order to reach the object of the invention, the present invention also provides a kind of Interactive Dynamic QTL based on biological cloud platform points
Analysis method, which comprises
Step 1, phenotypic data is imported and is analyzed, obtain the first processing data, execute step 3；
Step 2, screening and filtering is marked to genotype data, obtains second processing data, execute step 3；
Step 3, qtl analysis is carried out to the first processing data and second processing data, obtains the first analysis as a result, executing step
Rapid 4；
Step 4, judge whether the threshold value of the first analysis result meets expection；It is to then follow the steps 5；It is no, it thens follow the steps
6；
Step 5, analysis interpretation, export personality analysis report are carried out to the first analysis result；
Step 6, QTL interval threshold redefines, and executes step 3.
Optionally, phenotypic data is imported and is analyzed including one or more in following manner: to phenotypic data into
The one-touch Phenotype Distribution analysis of row and the analysis of one-touch phenotypic parameter；
Optionally, label screening filtering includes one or more in following manner: one-touch customized selected marker lacks
Mistake rate, one-touch customized selection minimum mark genetic distance and one-touch customized selection minimum mark physical distance；
Qtl analysis includes one or more in following manner: one-touch qtl analysis software selection, the choosing of one-touch mode
It selects, one-touch parameter selection, one-touch qtl analysis whole result are shown and the enrichment analysis of the function of the one-touch section QTL gene；
Wherein parameter specifically includes: threshold value, LOD confidence interval；
QTL interval threshold is redefined including one or more in following manner: parameter selection, the function in the section QTL
Enrichment analysis, qtl analysis whole result are shown and the function of the section QTL gene is enriched with analysis；Wherein parameter specifically includes: threshold
Value, LOD confidence interval.
In order to reach the object of the invention, the present invention provides a kind of Interactive Dynamic qtl analysis based on biological cloud platform
Method, which comprises
Step 1, phenotypic data is imported and is analyzed, obtain the first processing result；Execute step 3；
Step 2, screening and filtering is marked to genotype data, obtains second processing result；Execute step 3；
Step 3, qtl analysis is carried out to the first processing data and second processing data, obtains the first analysis result；Execute step
Rapid 4；
Step 4, the first analysis result is handled using sequence tools.
Optionally, phenotypic data is imported and is analyzed including one or more in following manner: to phenotypic data
Carry out one-touch Phenotype Distribution analysis and the analysis of one-touch phenotypic parameter；
Optionally, label screening filtering includes one or more in following manner: one-touch customized selected marker lacks
Mistake rate, one-touch customized selection minimum mark genetic distance and one-touch customized selection minimum mark physical distance；
Qtl analysis includes one or more in following manner: one-touch qtl analysis software selection, the choosing of one-touch mode
It selects, one-touch parameter selection, one-touch qtl analysis whole result are shown and the enrichment analysis of the function of the one-touch section QTL gene；
Wherein parameter specifically includes: threshold value, LOD confidence interval；
Sequence tools include one or more in following manner: genome browser, Blast is compared and design of primers；
Wherein, genome browser includes: to show gene structure in section, the abrupt information of parent and sequence downloading.
It optionally, further include step 5 between step 3,4；
Step 5, QTL interval threshold redefines.
Optionally, QTL interval threshold is redefined including one or more in following manner: parameter selection, the section QTL
Function enrichment analysis, qtl analysis whole result show and the section QTL gene function be enriched with analysis；Wherein parameter is specifically wrapped
It includes: threshold value, LOD confidence interval.
It is an advantage of the current invention that through the invention based on the Interactive Dynamic qtl analysis system of biological cloud platform and side
Method, level of integrated system is high, user-friendly, and phenotypic data, genotype data, qtl analysis can be set with one-touch parameter
It sets batch and completes correlation analysis content, reduce analysis threshold, promote user experience.
Detailed description of the invention
Fig. 1 is that the structure of the Interactive Dynamic qtl analysis system provided in an embodiment of the present invention based on biological cloud platform is shown
It is intended to；
Fig. 2 is the specific knot of the Interactive Dynamic qtl analysis system provided in an embodiment of the present invention based on biological cloud platform
Structure schematic diagram；
Fig. 3 is that the process of the Interactive Dynamic qtl analysis method provided in an embodiment of the present invention based on biological cloud platform is shown
It is intended to；
Fig. 4 is the another stream of the Interactive Dynamic qtl analysis method provided in an embodiment of the present invention based on biological cloud platform
Journey schematic diagram.
Specific embodiment
With reference to the accompanying drawings and examples, specific embodiments of the present invention will be described in further detail.Implement below
Example is not intended to limit the scope of the invention for illustrating the present invention.
As shown in Figs. 1-2, the embodiment of the present invention provides a kind of Interactive Dynamic qtl analysis system based on biological cloud platform
System, the system comprises but be not limited to: interactive analysis display module, interactive molecule intelligent screening module and Interactive Dynamic
Qtl analysis module；
Interactive analysis display module obtains the first processing data for being imported and being analyzed to phenotypic data；
Interactive molecule intelligent screening module obtains second processing for screening and filtering to be marked to genotype data
Data；
Interactive Dynamic qtl analysis module, for carrying out qtl analysis to the first processing data and second processing data.
Optionally, the first processing data here are specifically as follows phenotypic data, and second processing data are specifically as follows base
Because of type data.
Optionally, import with analysis include, but are not limited to, the following ways in it is one or more: one-touch Phenotype Distribution divide
Analysis and the analysis of one-touch phenotypic parameter；It can specifically be but not limited to that one-touch phenotype is arranged in interactive analysis display module
Distributional analysis unit and one-touch phenotypic parameter analytical unit.
Optionally, label screening filtering include, but are not limited to, the following ways in it is one or more: one-touch customized choosing
Select label miss rate, one-touch customized selection minimum mark genetic distance and one-touch customized selection minimum mark physics away from
From；It can specifically be but not limited to that one-touch customized selected marker miss rate is arranged in interactive molecule intelligent screening module
Unit, one-touch customized selection minimum mark genetic distance unit and one-touch customized selection minimum mark physical distance list
Member.
Optionally, qtl analysis include, but are not limited to, the following ways in it is one or more: the choosing of one-touch qtl analysis software
It selects, one-touch model selection, one-touch parameter selection, one-touch qtl analysis whole result is shown and the one-touch section QTL gene
Function be enriched with analysis；Wherein parameter is specifically including but not limited to: threshold value, LOD confidence interval.
Interactive analysis display module is specifically as genetic breeding phenotypic data automated analysis and result visualization show mould
Block, by one-touch Phenotype Distribution analysis and one-touch phenotypic parameter analysis etc., for user realize phenotypic data importing with point
Analyse function.Wherein Phenotype Distribution analysis includes but is not limited to: Phenotype Distribution frequency histogram and fit line, Phenotype Distribution case line
Figure, Phenotype Distribution correlation thermal map, after analysis can upload data by user, customized several phenotypic numbers of selection system are realized
Dynamically personalized analysis.Wherein phenotypic parameter analysis includes but is not limited to: missing values processing method, outlier processing method, more
The customized selections of parameters such as year more ground data processing (include but is not limited to average or BLUP seeks breeding value)；Meanwhile it analyzing
Acquired results figure, font can one-touch modification and downloadings.
Interactive molecule intelligent screening module is specifically as molecular labeling intelligent screening module passes through one-touch customized selection
Mark miss rate, one-touch customized selection minimum mark genetic distance, one-touch customized selection minimum mark physical distance
The parameter of equal label screenings filtering such as genetic map label filtering, guarantees label controllability and removal impurity label, realizes heredity
Map label filtering, simultaneity factor can realize mark information result visualization, obtain genetic map schematic diagram and all sample bases
Because of type information.
Interactive Dynamic qtl analysis module, is developed based on R/qtl, and user can customize parameter (including but not limited to LOD
Threshold value selection, permutation test number, the threshold value of permutation test, confidence interval etc.), be completed at the same time the section QTL gene information automatically
Extraction and GO/KEGG enrichment analysis；Such as by way of Web page picture, user can interact on same map
It checks QTL positioning result and carries out the comparison of multiple character positioning results；System is interacted using Javascript and user,
In QTL interaction analysis module, user can select to analyze accordingly according to their own needs, and including but not limited to LOD schemes (property
Shape+chromosome), the threshold value etc. in the section QTL and related gene parsing, each character QTL detection setting, and corresponding analysis exhibition can be downloaded
The file formats such as the png or svg of diagram are into local.
Preferably, which can be based on existing biological cloud platform；The system, can be in addition to above three big modules
There are blast comparison, design primer, genome browser (can show under gene structure in section, the abrupt information of parent, sequence
Carry) etc. modules corresponding to auxiliary functions.
The present invention has the advantages that at least three following:
(1) level of integrated system is high: various data can be stored in the system for a long time, log in use at any time at any time, and be
System user can upload the phenotypic data newly collected at any time and can long-term preservation.
(2) system one-touch can be analyzed: the multinomial analysis content such as various data, qtl analysis can one-touch batch
Correlation analysis is completed, the analysis work that professional analysis of biological information personnel complete is formerly only available, present system user uploads data
Afterwards, experimental data can be realized and excavate and parse, and generate a by choosing system corresponding analysis option, custom parameter
Propertyization analyzes result.
(3) system can also contain input-output file explanation, analysis parameter declaration, the system in addition to the above two o'clock
The corresponding module such as operation Video tutorials, it is user-friendly.
As shown in figure 3, the embodiment of the present application also provides a kind of Interactive Dynamic qtl analysis side based on biological cloud platform
Method, which comprises
Step S301, imports phenotypic data and is analyzed, and the first processing data are obtained, and executes step S303；
Optionally, it includes one or more in following manner for importing with analysis: one-touch Phenotype Distribution analysis and a key
The analysis of formula phenotypic parameter；
Screening and filtering is marked to genotype data in step S302, obtains second processing data, executes step S303；
Optionally, label screening filtering includes one or more in following manner: one-touch customized selected marker lacks
Mistake rate, one-touch customized selection minimum mark genetic distance and one-touch customized selection minimum mark physical distance etc.；
Step S303 carries out qtl analysis to the first processing data and second processing data, obtains the first analysis as a result, holding
Row step S304；
Optionally, qtl analysis includes one or more in following manner: one-touch qtl analysis software selects, is one-touch
Model selection, one-touch parameter selection, one-touch qtl analysis whole result is shown and the function of the one-touch section QTL gene is rich
Set analysis；Wherein parameter specifically includes: threshold value, LOD confidence interval；
Step S304, judges whether the threshold value of the first analysis result meets expection；It is to then follow the steps S305；It is no, then it holds
Row step S306；
Step S305, further progress analysis are interpreted: being carried out analysis interpretation to the first analysis result, exported personality analysis
Report；
Step S306, QTL interval threshold redefines, and executes step S303；
Optionally, QTL interval threshold is redefined including one or more in following manner: parameter selection, the section QTL
Function enrichment analysis, qtl analysis whole result show and the section QTL gene function be enriched with analysis；Wherein parameter is specifically wrapped
It includes: threshold value, LOD confidence interval.
Through the foregoing embodiment it is found that Interactive Dynamic QTL network analysis process is as follows in the present invention: by sample Phenotype Number
According to importing and analyzing, the filtering of genetic map label, then carry out qtl analysis, obtain whether result judgment threshold meets, if not
Satisfaction can carry out one-touch parameter selection in system, and change QTL interval threshold such as QTL interval threshold redefines, until obtaining
Expected results are obtained, experimental data is completed and excavates and further analyze, can finally export personality analysis report.
As shown in figure 4, the embodiment of the present application also provides a kind of Interactive Dynamic qtl analysis side based on biological cloud platform
Method, which comprises
Step 401, phenotypic data is imported and is analyzed, obtain the first processing result；Execute step 403；
Optionally, it includes one or more in following manner for importing with analysis: one-touch Phenotype Distribution analysis and a key
Formula phenotypic parameter analysis etc.；
Wherein Phenotype Distribution analysis includes but is not limited to: Phenotype Distribution frequency histogram and fit line, Phenotype Distribution case line
Figure, Phenotype Distribution correlation thermal map, after analysis can upload data by user, customized several phenotypic numbers of selection system are realized
Dynamically personalized analysis.Wherein phenotypic parameter analysis includes but is not limited to: missing values processing method, outlier processing method, more
The customized selections of parameters such as year more ground data processing (include but is not limited to average or BLUP seeks breeding value)；Meanwhile it analyzing
Acquired results figure, font can one-touch modification and downloadings；In addition, label screening filtering can also include: it is customized screening,
BLUP analysis etc.；
Step 402, screening and filtering is marked to genotype data, obtains second processing result；Execute step 403；
Optionally, label screening filtering includes one or more in following manner: one-touch customized selected marker lacks
Mistake rate, one-touch customized selection minimum mark genetic distance and one-touch customized selection minimum mark physical distance；
Pass through one-touch customized selected marker miss rate, one-touch customized selection minimum mark genetic distance, a key
The parameter of the label screenings filterings such as the customized selection minimum mark physical distance of formula such as genetic map label filtering, guarantees that label can
Control property and removal impurity label, realize genetic map label filtering, and simultaneity factor can realize mark information result visualization, obtain
Genetic map schematic diagram and all sample genotype informations；Wherein mark information result visualization specifically includes type statistics, figure
Spectrum etc.；In addition, label screening filtering can also include: group types and customized screening；
Optionally, qtl analysis includes one or more in following manner: one-touch qtl analysis software selects, is one-touch
Model selection, one-touch parameter selection, one-touch qtl analysis whole result is shown and the function of the one-touch section QTL gene is rich
Set analysis；Wherein parameter specifically includes: threshold value, LOD confidence interval；
Step 403, qtl analysis is carried out to the first processing data and second processing data, obtains the first analysis result；It executes
Step 404；
Step 404, the first analysis result is handled using sequence tools.
Optionally, sequence tools include one or more in following manner: genome browser, Blast are compared and are drawn
Object design；Wherein, genome browser includes: to show gene structure in section, the abrupt information of parent and sequence downloading.
It optionally, further include step 405 between step 403,404；
Step 405, QTL interval threshold redefines.
Optionally, QTL interval threshold is redefined including one or more in following manner: parameter selection, the section QTL
Function enrichment analysis, qtl analysis whole result show and the section QTL gene function be enriched with analysis；Wherein parameter is specifically wrapped
It includes: threshold value, LOD confidence interval.
Through the foregoing embodiment it is found that the present invention has the advantages that below at least three:
(1) level of integrated system is high: various data can be stored in the system for a long time, log in use at any time at any time, and be
System user can upload the phenotypic data newly collected at any time and can long-term preservation.
(2) system one-touch can be analyzed: the multinomial analysis content such as various data, qtl analysis can one-touch batch
Correlation analysis is completed, the analysis work that professional analysis of biological information personnel complete is formerly only available, present system user uploads data
Afterwards, experimental data can be realized and excavate and parse, and generate a by choosing system corresponding analysis option, custom parameter
Propertyization analyzes result.
(3) system can also contain input-output file explanation, analysis parameter declaration, the system in addition to the above two o'clock
The corresponding module such as operation Video tutorials, it is user-friendly.
The above is only a preferred embodiment of the present invention, it is noted that for the ordinary skill people of the art
For member, without departing from the technical principles of the invention, several improvement and replacement can also be made, these are improved and replacement
Also it should be regarded as protection scope of the present invention.
Claims (8)
1. a kind of Interactive Dynamic qtl analysis system based on biological cloud platform, which is characterized in that the system comprises: interaction
Formula analyzes display module, interactive molecule intelligent screening module and Interactive Dynamic qtl analysis module；
Interactive analysis display module obtains the first processing data for being imported and being analyzed to phenotypic data；
Interactive molecule intelligent screening module obtains second processing data for screening and filtering to be marked to genotype data；
Interactive Dynamic qtl analysis module, for carrying out qtl analysis to the first processing data and second processing data.
2. the system as claimed in claim 1, which is characterized in that
Phenotypic data is imported and analyzed including one or more in following manner: one-touch table is carried out to phenotypic data
Type distributional analysis and the analysis of one-touch phenotypic parameter；
Label screening filtering includes one or more in following manner: one-touch customized selected marker miss rate, one-touch
Customized selection minimum mark genetic distance and one-touch customized selection minimum mark physical distance；
Qtl analysis includes one or more in following manner: one-touch qtl analysis software selection, one-touch model selection, one
Keyed parameter selection, one-touch qtl analysis whole result are shown and the function of the one-touch section QTL gene is enriched with analysis；Wherein
Parameter specifically includes: threshold value, LOD confidence interval.
3. a kind of Interactive Dynamic qtl analysis method based on biological cloud platform, which is characterized in that the described method includes:
Step 1, phenotypic data is imported and is analyzed, obtain the first processing data, execute step 3；
Step 2, screening and filtering is marked to genotype data, obtains second processing data, execute step 3；
Step 3, qtl analysis is carried out to the first processing data and second processing data, obtains the first analysis as a result, executing step 4；
Step 4, judge whether the threshold value of the first analysis result meets expection；It is to then follow the steps 5；It is no, then follow the steps 6；
Step 5, analysis interpretation, export personality analysis report are carried out to the first analysis result；
Step 6, QTL interval threshold redefines, and executes step 3.
4. method as claimed in claim 3, which is characterized in that
Phenotypic data is imported and is analyzed including one or more in following manner: carrying out one-touch phenotype to phenotypic data
Distributional analysis and the analysis of one-touch phenotypic parameter.
Label screening filtering includes one or more in following manner: one-touch customized selected marker miss rate, one-touch
Customized selection minimum mark genetic distance and one-touch customized selection minimum mark physical distance；
Qtl analysis includes one or more in following manner: one-touch qtl analysis software selection, one-touch model selection, one
Keyed parameter selection, one-touch qtl analysis whole result are shown and the function of the one-touch section QTL gene is enriched with analysis；Wherein
Parameter specifically includes: threshold value, LOD confidence interval；
QTL interval threshold is redefined including one or more in following manner: parameter selection, the enrichment of the function in the section QTL
Analysis, qtl analysis whole result are shown and the function of the section QTL gene is enriched with analysis；Wherein parameter specifically includes: threshold value, LOD
Confidence interval.
5. a kind of Interactive Dynamic qtl analysis method based on biological cloud platform, which is characterized in that the described method includes:
Step 1, phenotypic data is imported and is analyzed, obtain the first processing result；Execute step 3；
Step 2, screening and filtering is marked to genotype data, obtains second processing result；Execute step 3；
Step 3, qtl analysis is carried out to the first processing data and second processing data, obtains the first analysis result；Execute step 4；
Step 4, the first analysis result is handled using sequence tools.
6. method as claimed in claim 5, which is characterized in that
Phenotypic data is imported and is analyzed including one or more in following manner: carrying out one-touch phenotype to phenotypic data
Distributional analysis and the analysis of one-touch phenotypic parameter.
Label screening filtering includes one or more in following manner: one-touch customized selected marker miss rate, one-touch
Customized selection minimum mark genetic distance and one-touch customized selection minimum mark physical distance；
Qtl analysis includes one or more in following manner: the selection of qtl analysis software, model selection, parameter selection, QTL points
Whole result is analysed to show and the enrichment analysis of the function of the section QTL gene；Wherein parameter specifically includes: threshold value, LOD confidence interval；
Sequence tools include one or more in following manner: genome browser, Blast is compared and design of primers；Wherein,
Genome browser includes: to show gene structure in section, the abrupt information of parent and sequence downloading.
7. method as claimed in claim 6, which is characterized in that
It further include step 5 between step 3,4；
Step 5, QTL interval threshold redefines.
8. the method for claim 7, which is characterized in that
QTL interval threshold is redefined including one or more in following manner: parameter selection, the enrichment of the function in the section QTL
Analysis, qtl analysis whole result are shown and the function of the section QTL gene is enriched with analysis；Wherein parameter specifically includes: threshold value, LOD
Confidence interval.
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