CN109166602A - The macro gene alaysis system of the microorganism of kitchen waste aerobic compost and method - Google Patents
The macro gene alaysis system of the microorganism of kitchen waste aerobic compost and method Download PDFInfo
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- CN109166602A CN109166602A CN201810992690.1A CN201810992690A CN109166602A CN 109166602 A CN109166602 A CN 109166602A CN 201810992690 A CN201810992690 A CN 201810992690A CN 109166602 A CN109166602 A CN 109166602A
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- 244000005700 microbiome Species 0.000 title claims abstract description 57
- 238000000034 method Methods 0.000 title claims abstract description 35
- 239000002361 compost Substances 0.000 title claims abstract description 23
- 108090000623 proteins and genes Proteins 0.000 title claims abstract description 19
- 239000010806 kitchen waste Substances 0.000 title claims abstract description 17
- 238000004458 analytical method Methods 0.000 claims abstract description 101
- 230000008569 process Effects 0.000 claims description 14
- 238000012252 genetic analysis Methods 0.000 claims description 8
- 238000010276 construction Methods 0.000 claims description 5
- 230000007246 mechanism Effects 0.000 claims description 5
- 230000004044 response Effects 0.000 claims description 5
- 238000012163 sequencing technique Methods 0.000 claims description 5
- 239000000284 extract Substances 0.000 claims description 4
- 235000013399 edible fruits Nutrition 0.000 claims description 3
- 238000004891 communication Methods 0.000 claims description 2
- 241000894006 Bacteria Species 0.000 description 4
- 108020004414 DNA Proteins 0.000 description 4
- 241000186046 Actinomyces Species 0.000 description 3
- 241000233866 Fungi Species 0.000 description 3
- 238000007405 data analysis Methods 0.000 description 3
- 238000011900 installation process Methods 0.000 description 3
- 239000002773 nucleotide Substances 0.000 description 3
- 125000003729 nucleotide group Chemical group 0.000 description 3
- 241000305071 Enterobacterales Species 0.000 description 2
- 241001655322 Streptomycetales Species 0.000 description 2
- 239000000090 biomarker Substances 0.000 description 2
- 229920002678 cellulose Polymers 0.000 description 2
- 239000001913 cellulose Substances 0.000 description 2
- 238000009264 composting Methods 0.000 description 2
- 238000013479 data entry Methods 0.000 description 2
- 238000010586 diagram Methods 0.000 description 2
- 230000000694 effects Effects 0.000 description 2
- 238000005516 engineering process Methods 0.000 description 2
- 238000003920 environmental process Methods 0.000 description 2
- 238000006116 polymerization reaction Methods 0.000 description 2
- 210000003705 ribosome Anatomy 0.000 description 2
- 102000053602 DNA Human genes 0.000 description 1
- 108091034117 Oligonucleotide Proteins 0.000 description 1
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- 230000009286 beneficial effect Effects 0.000 description 1
- 230000005540 biological transmission Effects 0.000 description 1
- 230000015572 biosynthetic process Effects 0.000 description 1
- 238000004364 calculation method Methods 0.000 description 1
- 230000015556 catabolic process Effects 0.000 description 1
- 239000003795 chemical substances by application Substances 0.000 description 1
- 230000000295 complement effect Effects 0.000 description 1
- 238000000354 decomposition reaction Methods 0.000 description 1
- 230000007423 decrease Effects 0.000 description 1
- 238000006731 degradation reaction Methods 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 238000002474 experimental method Methods 0.000 description 1
- 239000003337 fertilizer Substances 0.000 description 1
- 230000006870 function Effects 0.000 description 1
- 229920005610 lignin Polymers 0.000 description 1
- 229920002521 macromolecule Polymers 0.000 description 1
- 238000012423 maintenance Methods 0.000 description 1
- 230000002906 microbiologic effect Effects 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 108020004707 nucleic acids Proteins 0.000 description 1
- 102000039446 nucleic acids Human genes 0.000 description 1
- 150000007523 nucleic acids Chemical class 0.000 description 1
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- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Abstract
This application involves the macro gene alaysis systems of microorganism and method of a kind of kitchen waste aerobic compost, belong to bioinformatics technique field, which includes: that browser obtains target organism label, target primer sequence and target high-flux sequence data；Server splits the target high-flux sequence data according to target organism label and target primer sequence, obtains at least one set of biological sequence；At least one set of biological sequence is analyzed by least two analysis of biological information tools, obtains at least two analysis results；It is analyzed by adhesion program adhesion at least two as a result, obtaining biological classification report；Biological classification is reported by multivariate mathematical analysis and carries out the analysis of key microorganisms species, obtains analysis result；Analysis result is sent to browser to show；The analysis efficiency of the macro gene of microorganism can be improved, reduce analysis difficulty.
Description
Technical field
The present invention relates to the macro gene alaysis systems of microorganism and method of a kind of kitchen waste aerobic compost, belong to biology
Informatics technical field.
Background technique
Microorganism metagenomics are a kind of exploration complex environment sample such as compost, soil, bottoms developed in recent years
The cutting edge technology system of microbiological paper method and process in mud etc..Microorganism metagenomics can be in single experiment simultaneously
Hundreds to thousands sample is detected, the data volume of generation reaches 50-60 gigabyte (Gigabyte, Gb), supreme containing several ten million
Hundred million gene orders, based on said gene sequence can systematically analyze in the samples such as compost microorganism group at and Fauna construction and
To the response mechanism of varying environment process, the resourcable transformation for kitchen waste and the research and development using technology provide most important theories
Guidance.
Microorganism metagenomics can disclose microorganism dynamic process in complex system.But since data volume is big, data
Analysis is difficult, often requires to use a variety of analysis of biological information tools.Currently, analysis of biological information tool include QIIME,
Mothur, ribosomes database project (Ribosomal database project, RDP) Naive Bayes Classifier (RDP
Naive bayes classifier), R program etc..
Current analysis of biological information tool needs carry out calculation by program on linux system, need biometrics, biology
Various comprehensive knowledges such as information and computer system maintenance.And the installation process complexity of most analysis of biological information tools,
Usually need to be programmed in use process, therefore, requirement to the biological information, computer capacity of data analyst compared with
It is high.In addition, different data analysts is different to the understanding of microorganism metagenomics data, data analysis process is easy to produce
Raw difference is unfavorable for standardizing the implementation of process and subsequent trace analysis.
Summary of the invention
The purpose of the present invention is to provide a kind of macro gene alaysis system of microorganism of kitchen waste aerobic compost and sides
Method.In order to achieve the above objectives, the invention provides the following technical scheme:
In a first aspect, providing a kind of macro gene alaysis system of microorganism of kitchen waste aerobic compost, the system
The browser for including: server and being connected with the server communication；
The browser, target organism label, target primer sequence and target high pass for obtaining user's input measure
Ordinal number evidence；The target organism label, the target primer sequence and the target high-flux sequence data are sent to described
Server；
The server, it is high-throughput for receiving the target organism label, the target primer sequence and the target
Sequencing data；The target high-flux sequence data are torn open according to the target organism label and the target primer sequence
Point, obtain at least one set of biological sequence；At least one set of biological sequence is divided by least two analysis of biological information tools
Analysis, obtains at least two analysis results；By at least two analyses described in adhesion language adhesion as a result, obtaining biological classification report
It accuses；The biological classification is reported by multivariate mathematical analysis and carries out the analysis of key microorganisms species, obtains analysis result；It will
The analysis result is sent to the browser；
The browser, for showing the analysis result.
Optionally, the server is based on using galaxy developing instrument using expandable mark language XML language
Needle Wunschman model integrated data splitting tool, the data splitting tool are described according to the target for executing
Biomarker and target primer sequence split polygenes mixing metagenomics sequencing data, obtain at least one set of biology
The step of sequence.
Optionally, at least two analysis of biological information tool include: Usearch, Qiime, Mothur, BLASTN and
The driver of at least two open source softwares in RDP Naive Bayes Classifier.
Optionally, the adhesion language includes that practical report extracts at least one of language Perl and Python.
Optionally, the server, is used for: being analyzed using R language by multivariate mathematical and is reported the biological classification
Carry out the analysis of key microorganisms kind.
Optionally, the browser, is used for: showing the analysis result by diagrammatic form.
Optionally, the analysis result includes:
Microorganism group is at, the Fauna construction of microorganism and microorganism to the response mechanism of varying environment process in compost sample
At least one of.
Second aspect provides a kind of macro genetic analysis method of microorganism of kitchen waste aerobic compost, for servicing
In device, which comprises
Receive target organism label, target primer sequence and target high-flux sequence data that browser is sent；
The target high-flux sequence data are split according to the target organism label and target primer sequence, are obtained
To at least one set of biological sequence；
At least one set of biological sequence is analyzed by least two analysis of biological information tools, obtains at least two points
Analyse result；
By at least two analyses described in adhesion language adhesion as a result, obtaining biological classification report；
The biological classification is reported by multivariate mathematical analysis and carries out the analysis of key microorganisms species, obtains analysis knot
Fruit；
The analysis result is sent to the browser.
The third aspect provides a kind of macro genetic analysis method of microorganism of kitchen waste aerobic compost, for browsing
In device, which comprises
Obtain target organism label, target primer sequence and the target high-flux sequence data of user's input；
The target organism label, the target primer sequence and the target high-flux sequence data are sent to described
Server, the target organism label and the target primer sequence are used for for the server to the target high-flux sequence
Data are split, and at least one set of biological sequence is obtained；By at least two analysis of biological information tools at least one set of biology
Sequence is analyzed, and at least two analysis results are obtained；By at least two analyses described in adhesion language adhesion as a result, being given birth to
Object classification report；The biological classification is reported by multivariate mathematical analysis and carries out the analysis of key microorganisms species, is divided
Analyse result；
Receive and show the analysis result that the server is sent.
The beneficial effects of the present invention are: by receiving the target organism label of browser transmission by server, target is drawn
Object sequence and target high-flux sequence data, and according to target organism label and target primer sequence to target high-flux sequence number
According to being split, at least one set of biological sequence is obtained；By at least two analysis of biological information tools at least one set of Biological Order
Column are analyzed, and at least two analysis results are obtained；It is analyzed by adhesion language adhesion at least two as a result, obtaining biological classification
Report；Biological classification is reported by multivariate mathematical analysis and carries out the analysis of key microorganisms species, obtains analysis result；It will divide
Analysis result is sent to browser and is shown by browser；It can solve the installation process complexity of analysis of biological information tool, use
It usually needs to be programmed in the process, micro- life can be improved in the problem for causing the analytic process efficiency of the macro gene of microorganism lower
The analysis efficiency of the macro gene of object.
The above description is only an overview of the technical scheme of the present invention, in order to better understand the technical means of the present invention,
And can be implemented in accordance with the contents of the specification, the following is a detailed description of the preferred embodiments of the present invention and the accompanying drawings.
Detailed description of the invention
Fig. 1 is the macro gene alaysis system of microorganism for the kitchen waste aerobic compost that the application one embodiment provides
Structural schematic diagram；
Fig. 2 is the macro genetic analysis method of microorganism for the kitchen waste aerobic compost that the application one embodiment provides
Flow chart.
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.
Fig. 1 is the macro genetic analysis system of the microorganism for kitchen waste aerobic compost that the application one embodiment provides
The structural schematic diagram of system, as shown in Figure 1, the system includes at least: server 110 and browser 120.
Browser 120, for obtaining target organism label, target primer sequence and the target high-flux sequence of user's input
Data；Target organism label, target primer sequence and target high-flux sequence data are sent to server.
Server 110, for receiving target organism label, target primer sequence and target high-flux sequence data；According to
Target organism label and target primer sequence split target high-flux sequence data, obtain at least one set of biological sequence；
At least one set of biological sequence is analyzed by least two analysis of biological information tools, obtains at least two analysis results；
It is analyzed by adhesion language adhesion at least two as a result, obtaining biological classification report；By multivariate mathematical analysis to biology point
Class report carries out the analysis of key microorganisms species, obtains analysis result；Analysis result is sent to browser.
Browser 120, for showing analysis result.
Optionally, server 110 is based on Needle using expandable mark language XML language using galaxy developing instrument
Wunschman model integrated data splitting tool, the data splitting tool draw for executing according to target organism label and target
The step of object sequence splits to polygenes mixing metagenomics sequencing data, obtains at least one set of biological sequence.
Optionally, at least two analysis of biological information tools include: Usearch, Qiime, Mothur, BLASTN and RDP
The driver of at least two open source softwares in Naive Bayes Classifier.
Optionally, adhesion language includes that practical report extracts at least one of language Perl and Python.
Optionally, server 110, which is used to analyze using R language by multivariate mathematical, reports that progress is crucial to biological classification
Microbial species analysis.
Optionally, browser 120, for showing analysis result by diagrammatic form.
Optionally, analysis result include: in compost sample microorganism group at, the Fauna construction of microorganism and microorganism to not
With at least one of the response mechanism of environmental process.
Fig. 2 is the macro genetic analysis method of microorganism for the kitchen waste aerobic compost that the application one embodiment provides
Flow chart, the present embodiment are illustrated so that this method is applied in system shown in FIG. 1 as an example.This method includes at least following
Several steps:
Step 201, browser obtains target organism label, target primer sequence and the target high-flux sequence of user's input
Data.
Optionally, biomarker (barcode) is used to uniquely identify the classification of microorganism.Microorganism can be for heap
The microorganism of fertilizer, such as: the present embodiment such as monad, streptomycete, enterobacteria will not enumerate herein.
Primer refers to when nucleotide polymerization is acted on and being originated, and stimulates a kind of big point with specific nucleotide sequence of synthesis
Son, the molecule being connect in the form of covalent bond with reactant.Primer is usually two artificial synthesized segment oligonucleotide sequences, and one is drawn
One DNA (deoxyribonucleic of object and target region one end
Acid, DNA) template strand complementation, another primer is complementary with another DNA template chain of the target region other end,
Function is the starting point as nucleotide polymerization effect.Primer sequence refers to the sequence of the gene in gene order including primer.
High-flux sequence data, which refer to, once carries out the number that sequencing obtains to millions of nucleic acid molecules to hundreds of thousands
According to.
Optionally, browser is provided with data entry controls, and user inputs target organism mark by the data entry controls
Label, target primer sequence and target high-flux sequence data.
Step 202, target organism label, target primer sequence and target high-flux sequence data are sent to clothes by browser
Business device.
Optionally, the quantity of target organism label can be at least one, the quantity of target primer sequence may be to
One few, the quantity to target organism label and the quantity of target primer sequence do not limit the present embodiment.
Step 203, target organism label, target primer sequence and the target high pass that server receives that browser is sent measure
Ordinal number evidence.
Step 204, server carries out target high-flux sequence data according to target organism label and target primer sequence
It splits, obtains at least one set of biological sequence.
Optionally, server is based on Needle using expandable mark language XML language using galaxy developing instrument
Wunschman model integrated data splitting tool, the data splitting tool draw for executing according to target organism label and target
The step of object sequence splits to target high-flux sequence data, obtains at least one set of biological sequence.
Needle Wunschman model is used to carry out the overall comparison of sequence.That is, attempting to find two complete sequences
Optimal comparison between S1 and S2.As if S1=GCCCTAGCG S2=GCGCAATG sets each matching character as 1 point, often
A space is -2 points, and each mismatch is -1 point, then following comparison is exactly that global optimum compares: S1'=GCCCTAGCG S2'
=GCGC_AATG, hyphen " _ " represent space.There are five matching character in S2', space (or exist conversely speaking,
Have an inserted term in S1'), there are three mismatch character.The score obtained in this way be (5 × 1)+(1 × -2)+(3 × -1)=
0, this optimum being that by.
Step 205, server analyzes at least one set of biological sequence by least two analysis of biological information tools,
Obtain at least two analysis results.
Optionally, at least two analysis of biological information tools include: Usearch, Qiime, Mothur, BLASTN and RDP
Naive Bayes Classifier.
Bioanalytical tools are for determining the classification of at least one set of biological sequence.
Step 206, server is analyzed by adhesion language adhesion at least two as a result, obtaining biological classification report.
Adhesion language includes that practical report extracts at least one of language Perl and Python.
Step 207, server is analyzed by multivariate mathematical and reports progress key microorganisms species analysis to biological classification,
Obtain analysis result.
Optionally, server is analyzed by multivariate mathematical using R language and reports progress key microorganisms to biological classification
Kind analysis.
Optionally, analysis result include: in compost sample microorganism group at, the Fauna construction of microorganism and microorganism to not
With at least one of the response mechanism of environmental process.
Such as: in composting process, bacteria abundance 2 orders of magnitude higher than fungi and actinomyces, but three is in composting process
The general morphologictrend of middle quantity is consistent, is first to rise to decline afterwards.Bacterium can be prevailing the reason is that it small in size,
Large specific surface area quickly can provide energy using solable matter for own growth and proliferation.In the temperature rise period of compost, by thermophilic
Warm microorganism decomposes organic matter, such as pseudomonad, streptomycete, enterobacteria.Into after high temperature period, height can adapt to
Bacterium, fungi and the actinomyces of warm condition continue to participate in the degradation to complicated macromolecular substances, such as cellulose, lignin, albumen
Matter etc., but when heap temperature is more than that 64 DEG C of fungi almost all disappear, actinomyces become the dominant bacteria of decomposition of cellulose.
Step 208, server is sent to browser for result is analyzed.
Step 209, the analysis result that browser receives and display server is sent.
Optionally, browser shows the analysis result by diagrammatic form.Such as: it is shown with chart and is risen under different temperatures
The microorganism type and quantity of effect.
In conclusion the macro genetic analysis method of the microorganism of kitchen waste aerobic compost provided in this embodiment, passes through
Target organism label, target primer sequence and the target high-flux sequence data sent by server reception browser, and according to
Target organism label and target primer sequence split target high-flux sequence data, obtain at least one set of biological sequence；
At least one set of biological sequence is analyzed by least two analysis of biological information tools, obtains at least two analysis results；
It is analyzed by adhesion language adhesion at least two as a result, obtaining biological classification report；By multivariate mathematical analysis to biology point
Class report carries out the analysis of key microorganisms species, obtains analysis result；Analysis result is sent to browser and is shown by browser
Show；The installation process that can solve analysis of biological information tool is complicated, usually needs to be programmed in use process, leads to micro- life
The lower problem of the analytic process efficiency of the macro gene of object, can be improved the analysis efficiency of the macro gene of microorganism.
In addition, the application is put down by a variety of bioinformatic tools of a series of programming language adhesion, and by galaxy
Platform has developed macro gene big data analysis platform, realizes directly to divide by browser and folds genome big data.While according to
According to the platform, without grasping complicated computer literacy, such as R, Perl programming language and a variety of bioinformatic tools, Ji Keshi
Existing agriculture gene big data point folding；Significantly reduce the difficulty using the technological development new microbe agent.
Optionally, the embodiment of the method that step 201,204-209 can be implemented separately as server side；Step 202,203 and
210 can be implemented separately as the embodiment of the method for browser side, and the present embodiment is not construed as limiting this.
Each technical characteristic of embodiment described above can be combined arbitrarily, for simplicity of description, not to above-mentioned reality
It applies all possible combination of each technical characteristic in example to be all described, as long as however, the combination of these technical characteristics is not deposited
In contradiction, all should be considered as described in this specification.
The embodiments described above only express several embodiments of the present invention, and the description thereof is more specific and detailed, but simultaneously
It cannot therefore be construed as limiting the scope of the patent.It should be pointed out that coming for those of ordinary skill in the art
It says, without departing from the inventive concept of the premise, various modifications and improvements can be made, these belong to protection of the invention
Range.Therefore, the scope of protection of the patent of the invention shall be subject to the appended claims.
Claims (9)
1. a kind of macro gene alaysis system of microorganism of kitchen waste aerobic compost, which is characterized in that the system comprises clothes
Business device and the browser being connected with the server communication:
The browser, for obtaining target organism label, target primer sequence and the target high-flux sequence number of user's input
According to；The target organism label, the target primer sequence and the target high-flux sequence data are sent to the service
Device；
The server, for receiving the target organism label, the target primer sequence and the target high-flux sequence
Data；The target high-flux sequence data are split according to the target organism label and the target primer sequence,
Obtain at least one set of biological sequence；At least one set of biological sequence is analyzed by least two analysis of biological information tools,
Obtain at least two analysis results；By at least two analyses described in adhesion language adhesion as a result, obtaining biological classification report；It is logical
It crosses multivariate mathematical analysis and reports progress key microorganisms species analysis to the biological classification, obtain analysis result；It will be described
Analysis result is sent to the browser；
The browser, for showing the analysis result.
2. system according to claim 1, which is characterized in that the server can be expanded using the use of galaxy developing instrument
It opens up mark language XML language and is based on Needle Wunschman model integrated data splitting tool, the data splitting tool is used
In execute it is described according to the target organism label and target primer sequence to polygenes mixing metagenomics sequencing data into
The step of row is split, and obtains at least one set of biological sequence.
3. system according to claim 1, it is characterised in that:
At least two analysis of biological information tool includes: Usearch, Qiime, Mothur, BLASTN and RDP simplicity pattra leaves
The driver of at least two open source softwares in this classifier.
4. system according to claim 1, it is characterised in that:
The adhesion language includes that practical report extracts at least one of language Perl and Python.
5. system according to claim 1, which is characterized in that the server is used for:
It is analyzed using R language by multivariate mathematical and reports progress key microorganisms kind analysis to the biological classification.
6. system according to any one of claims 1 to 5, which is characterized in that the browser is used for:
The analysis result is shown by diagrammatic form.
7. system according to any one of claims 1 to 5, which is characterized in that the analysis result includes:
Microorganism group is at, the Fauna construction of microorganism and microorganism in the response mechanism of varying environment process in compost sample
It is at least one.
8. a kind of macro genetic analysis method of the microorganism of kitchen waste aerobic compost, which is characterized in that be used in server, institute
The method of stating includes:
Receive target organism label, target primer sequence and target high-flux sequence data that browser is sent；
The target high-flux sequence data are split according to the target organism label and target primer sequence, obtain to
Few one group of biological sequence；
At least one set of biological sequence is analyzed by least two analysis of biological information tools, obtains at least two analysis knots
Fruit；
By at least two analyses described in adhesion language adhesion as a result, obtaining biological classification report；
The biological classification is reported by multivariate mathematical analysis and carries out the analysis of key microorganisms species, obtains analysis result；
The analysis result is sent to the browser.
9. a kind of macro genetic analysis method of the microorganism of kitchen waste aerobic compost, which is characterized in that be used in browser, institute
The method of stating includes:
Obtain target organism label, target primer sequence and the target high-flux sequence data of user's input；
The target organism label, the target primer sequence and the target high-flux sequence data are sent to the service
Device, the target organism label and the target primer sequence are used for for the server to the target high-flux sequence data
It is split, obtains at least one set of biological sequence；By at least two analysis of biological information tools at least one set of biological sequence
It is analyzed, obtains at least two analysis results；By at least two analyses described in adhesion language adhesion as a result, obtaining biology point
Class report；The biological classification is reported by multivariate mathematical analysis and carries out the analysis of key microorganisms species, obtains analysis knot
Fruit；
Receive and show the analysis result that the server is sent.
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| CN110033830A (en) * | 2019-04-16 | 2019-07-19 | 苏州金唯智生物科技有限公司 | A kind of data transmission method for uplink, device, equipment and storage medium |
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