CN105975811B - A kind of gene sequencing device intelligently compared - Google Patents
A kind of gene sequencing device intelligently compared Download PDFInfo
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- CN105975811B CN105975811B CN201610301745.0A CN201610301745A CN105975811B CN 105975811 B CN105975811 B CN 105975811B CN 201610301745 A CN201610301745 A CN 201610301745A CN 105975811 B CN105975811 B CN 105975811B
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- 108090000623 proteins and genes Proteins 0.000 title claims abstract description 199
- 238000012163 sequencing technique Methods 0.000 title claims abstract description 14
- 230000036541 health Effects 0.000 claims abstract description 63
- 238000004458 analytical method Methods 0.000 claims abstract description 32
- 238000002864 sequence alignment Methods 0.000 claims abstract description 20
- 238000011161 development Methods 0.000 claims description 16
- 239000011159 matrix material Substances 0.000 claims description 8
- 238000013507 mapping Methods 0.000 claims description 6
- 230000014509 gene expression Effects 0.000 claims description 4
- 230000015572 biosynthetic process Effects 0.000 claims description 3
- 238000013461 design Methods 0.000 claims description 3
- 230000007613 environmental effect Effects 0.000 claims description 2
- 230000005856 abnormality Effects 0.000 claims 1
- 238000004519 manufacturing process Methods 0.000 abstract description 2
- 230000001225 therapeutic effect Effects 0.000 abstract 1
- 238000005516 engineering process Methods 0.000 description 9
- 239000000284 extract Substances 0.000 description 4
- 238000000034 method Methods 0.000 description 4
- 239000008280 blood Substances 0.000 description 3
- 210000004369 blood Anatomy 0.000 description 3
- 230000006872 improvement Effects 0.000 description 2
- 230000002265 prevention Effects 0.000 description 2
- 238000004891 communication Methods 0.000 description 1
- 238000010586 diagram Methods 0.000 description 1
- 230000000694 effects Effects 0.000 description 1
- 238000012268 genome sequencing Methods 0.000 description 1
- 239000000463 material Substances 0.000 description 1
- 230000008569 process Effects 0.000 description 1
- 102000004169 proteins and genes Human genes 0.000 description 1
- 239000007921 spray Substances 0.000 description 1
- 208000024891 symptom Diseases 0.000 description 1
- 230000009466 transformation Effects 0.000 description 1
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
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Abstract
The invention discloses a kind of gene sequencing device intelligently compared, the present invention compares with module, four part of health analysis module comprising gene pool server, sequence alignment module, intelligence by the designing for gene pool stored to the various therapeutic equipments of hospital.The present apparatus is using a certain number of standard use-case genes as standard gene sequence, the gene order of individual subscriber is compared with standard gene sequence by certain comparison generation, similarity result is analyzed, obtaining the user, there are inferior health or unsound possibility conclusions, and provide production and living guidance, user can carry out intelligence with good friend and compare, obtain victory or defeat, the probability height for prompting the potential inferior health of gene of user with open arms with intelligent comparison result, causes the attention of user itself.
Description
Technical field
The present invention relates to the gene sequencing devices in a kind of national gene server, and in particular to one kind is based on base
Because of the intellectual analysis device of sequence alignment.
Background technique
Gene is the inhereditary material of organism, it determines the different trait expression of organism by specific coded sequence.People
The difficulty symptom such as many inferior healths of class, it is closely related with the gene of the mankind, if we can pass through the gene order of analysis people
It detects whether the possibility of potential inferior health occurs, then we can take measures in advance, prevention is or, to reach more
Good effect, is benefited for society.
The premise of the technology is gene sequencing technology and sequence alignment technology, with the rapid development base of biological information science
Because being sequenced and the technology of sequence alignment is very advanced, for the interest inferior health analytical technology that is compared based on gene order
Appearance provides possibility.
Currently, ripe day by day with two generation sequencing technologies, human genome sequencing declines from 3,000,000,000 U.S. dollars of beginning
To about 1000 U.S. dollars.The even lower whole gene group sequence a people is sequenced of hundreds of U.S. dollars will be realized in the near future.
Personalized gene sequencing, the industry relevant to genomic information such as inferior health analysis will be in well with the downward of sequencing price
Spray formula increases.
On the other hand, with the improvement of living standards, people become more concerned with healthy lifestyles, pass through gene
The guiding significance to healthy living that analysis obtains is compared also to be becoming increasingly popular.And plentiful, the meeting of people's life now
There are more people to be ready that money is taken to remove the gene that oneself is sequenced.
With emerging in large numbers for magnanimity biological data, pass through the personal biological information data in the server of lots of genes library
(gene, protein sequence) analysis and biological data will become new trend.
Summary of the invention
The present invention takes phase to detect the certain sub-health states determined by gene that may be in advance
The prevention of measure progress and protection are answered, a kind of gene sequencing device intelligently compared is provided, utilizes a certain number of standards
Use-case gene is generated as standard gene sequence, by the gene order of individual subscriber and standard gene sequence by certain comparison
Be compared, similarity result analyzed, obtain the user suffer from certain inferior health a possibility that conclusion, and provide health
Guidance and daily life suggestion.
The technical scheme adopted by the invention is as follows a kind of gene sequencing device intelligently compared, which is characterized in that packet
It includes:
Gene pool server, according to the gene order and standard use-case of different classes of, different degrees of storage individual subscriber
Gene order；
Sequence alignment module, for by the gene order of the gene order of individual subscriber and the standard use-case of corresponding classification
Similarity comparison is carried out, and returns to the similarity value with the gene order of standard use-case；
Intelligence compares with module, and the gene order for the same category between user is similar to the gene order of standard use-case
Degree compares with；
Health analysis module, for the gene order of the individual subscriber by analyzing a certain classification and the gene of standard use-case
The similarity of gene order of the sequence under in various degree, obtains the development trend of user health, and provide health guidance and
Daily life suggestion；
Gene pool server specifically includes: database storage unit, database control unit；
Database storage unit is led to for storing be mutually related " user ", " gene classification ", " performance degree " information
Reasonable database design is crossed, by the gene order of standard use-case and the gene order of individual subscriber and " performance degree " and " base
Because of classification " connection, the gene order of standard use-case and the gene order of individual subscriber are associated with " user "；Each user is only
The gene pool of oneself can be accessed, the gene order of the individual subscriber of other users and the gene pool of standard use-case cannot be accessed；
Database control unit such as is added to database storage unit, modifies, deleting at the operation；
Sequence alignment module includes: sequence alignment generation unit, gene order and the standard use-case for individual subscriber
Similarity comparison is carried out between gene order, and extracts and returns to the result that obtained similarity compares, and intelligence compares life
At the following steps are included:
Step 1: the two sequences for participating in comparing are divided to obtain the feature vector of ten points to alphabet is carried out；
Step 2: by the desired value of the data of the feature vector of ten points, according to formula:
Pass through the desired value k of the normal data of the gene order of standard use-caseiIt is calculated, obtains the base with individual subscriber
Because the feature of sequence is poor, Δ k is rememberedi, and k it is expected according to average data of the following equation to typical inferior healthaveValue by following
The score information of the i-th point of formula formation sequence:
Wherein e is natural constant；
Pass through obtained aiCreate scoring matrix；
Step 3: being given a mark according to obtained scoring matrix；
Step 4: to the two sequences for participating in comparing for being higher than certain threshold value obtained by step 3 to progress both ends extension；
Step 5: to the two sequences for participating in comparing for being higher than certain threshold value obtained by step 4 to assessing, obtaining
Last high score segment；
Counting statistics unit, for counting the high score segment obtained by step 5, and compared according to the participation for participating in comparing
The length gauge of two sequences pair calculates similarity value；
Intelligence compares with module and specifically includes:
Intelligent comparing unit, for carrying out the competition of same type gene between user, i.e., with the user in respective account
The comparison value of the gene order of personal gene order and standard use-case is to compare with foundation, is decided the winner by the height of score value, from
Obtained in score victor may to the gene expression character development trend it is bigger, be denoted as intelligent comparison result and record；
Health analysis module specifically includes:
Health analysis unit, in the respective account of user analyze individual subscriber gene order under corresponding classification
The comparison result value of the gene order of the standard use-case of whole degree, the purpose of comparison result value are to analyze the individual subscriber of user
Gene order it is whether similar with the gene order of certain inferior health, if similar, be denoted as A, and generate current individual subscriber body
Body state will reach time t required for this inferior health program1The time is typically lasted for possibility μ, and this inferior health
t2, according to different user characteristics similar A, t1And t2Mapped with this inferior health, mapping equation f (A) are as follows:
To obtain the potential inferior health development trend that user is determined by a certain type gene, and by potential inferior health
Development trend result returns；It, can be by mapping equation f since the gene order of individual subscriber is easy to produce variation by environmental Kuznets Curves
(A) to be stored in the circular linked list that can be inquired, for the matching of sequence table, in case of the exception of personal gene order
State just sends the result to guiding opinion unit；
Guiding opinion unit is instructed for what is obtained for health analysis unit as a result, providing reasonable healthy living,
And life production is suggested.
Detailed description of the invention
Fig. 1 is the structural diagram of the present invention；
Specific embodiment
In order to which technical problems, technical solutions and advantages to be solved are more clearly understood, tie below
Accompanying drawings and embodiments are closed, the present invention will be described in detail.It should be noted that specific embodiment described herein is only used
It to explain the present invention, is not intended to limit the present invention, the product for being able to achieve said function belongs to equivalent replacement and improvement, includes
Within protection scope of the present invention.The specific method is as follows:
Embodiment 1: as shown in Figure 1, the present invention may be implemented by the transformation of the gene pool stored to hospitalize equipment
Module, health analysis module are compared with comprising gene pool server, sequence alignment module, intelligence, totally four is most of.Gene pool service
Device, the gene order for gene order and individual subscriber by different classes of, different degrees of storage standard use-case；Sequence alignment
Module is compared for the gene order of individual subscriber to be carried out similarity with the gene order of the standard use-case of corresponding classification, and
Return to the similarity value with the gene order of the standard use-case of each degree；Intelligence compares with module, for identical between user
The similarity of the gene order of the gene order and standard use-case of classification compares with；Health analysis module, for passing through analysis user
A certain classification gene order and standard use-case gene order in various degree under gene order similarity, obtain user
The development trend of health, and provide health guidance and daily life suggestion.
The present embodiment should first be selected by technology using different inferior health genomical ways a certain number of enough before starting
Standard use-case patient groups extract blood sample, carry out the gene pool in the whole country by various communication modes and construct, and pass through tune
The gene order that will be obtained with gene pool server uploads to gene pool clothes according to different inferior healths, different performance degree
It is engaged in device.
User first has to that the gene order of oneself is sequenced in the various equipment of gene sequencing company or hospital, and be converted into
The file that the health analysis device requirement intelligently compared based on gene order is consistent.Then based on gene order intelligence ratio
Pair health analysis device registration account and log in, subsequently into the personal gene pool of the equipment individual center of hospital, according to phase
The gene classification answered uploads the gene order file of oneself, and the Database Unit in gene pool server uses corresponding behaviour at this time
Make method sequential file is saved in database, and with user account and gene category associations.
Sequence alignment generation unit in sequence alignment module, by database module by the individual subscriber under a certain classification
Gene order and the gene order of standard use-case checked out from database, gene order and each table individual subscriber
The gene order of standard use-case under existing degree is compared one by one.Detailed process is as follows: to participate in compare two sequences into
Row divides alphabet；Then reasonable scoring matrix is created；The gene order of two sequences compare one by one and basis is beaten
Sub-matrix marking；The obtained sequence higher than certain threshold value gives a mark again to progress both ends extension, higher than the sequence of certain threshold value
Column obtain last high score segment to assessing.Counting statistics unit calculates phase according to the length gauge for the sequence for participating in comparing
Like angle value, by the comparison result averaged under each performance degree, then the average value of each performance degree is using meter
It calculates and acquires respectively shared ratio, show that the probability of each performance degree is counted as final result, and be stored in data
In library, with user-association.
Gene pool server, according to the gene order and standard use-case of different classes of, different degrees of storage individual subscriber
Gene order；
Sequence alignment module, for by the gene order of the gene order of individual subscriber and the standard use-case of corresponding classification
Similarity comparison is carried out, and returns to the similarity value with the gene order of standard use-case；
Intelligence compares with module, and the gene order for the same category between user is similar to the gene order of standard use-case
Degree compares with；
Health analysis module, for the gene order of the individual subscriber by analyzing a certain classification and the gene of standard use-case
The similarity of gene order of the sequence under in various degree, obtains the development trend of user health, and provide health guidance and
Daily life suggestion；
Gene pool server specifically includes: database storage unit, database control unit；
Database storage unit is led to for storing be mutually related " user ", " gene classification ", " performance degree " information
Reasonable database design is crossed, by the gene order of standard use-case and the gene order of individual subscriber and " performance degree " and " base
Because of classification " connection, the gene order of standard use-case and the gene order of individual subscriber are associated with " user "；Each user is only
The gene pool of oneself can be accessed, the gene order of the individual subscriber of other users and the gene pool of standard use-case cannot be accessed；
Database control unit such as is added to database storage unit, modifies, deleting at the operation；
Sequence alignment module includes: sequence alignment generation unit, gene order and the standard use-case for individual subscriber
Similarity comparison is carried out between gene order, and extracts and returns to the result that obtained similarity compares, and intelligence compares life
At the following steps are included:
Step 1: the two sequences for participating in comparing are divided to obtain the feature vector of ten points to alphabet is carried out；
Step 2: by the desired value of the data of the feature vector of ten points, according to formula:
Pass through the desired value k of the normal data of the gene order of standard use-caseiIt is calculated, obtains the base with individual subscriber
Because the feature of sequence is poor, Δ k is rememberedi, and k it is expected according to average data of the following equation to typical inferior healthaveValue by following
The score information of the i-th point of formula formation sequence:
Wherein e is natural constant；
Pass through obtained aiCreate scoring matrix；
Step 3: being given a mark according to obtained scoring matrix；
Step 4: to the two sequences for participating in comparing for being higher than certain threshold value obtained by step 3 to progress both ends extension；
Step 5: to the two sequences for participating in comparing for being higher than certain threshold value obtained by step 4 to assessing, obtaining
Last high score segment；
Counting statistics unit, for counting the high score segment obtained by step 5, and compared according to the participation for participating in comparing
The length gauge of two sequences pair calculates similarity value；
User software platform searches for other users, and adds as a friend mutually, then intelligence can be used and compare with module progress phase
The competition of generic gene.Intelligence compares with the gene comparison result of the same category of two users of intelligent comparing unit in module
It is compared, obtains victory or defeat, prompt the probability height of the potential illness of gene of user with open arms with intelligent comparison result, cause to use
The attention at family itself.
Intelligence compares with module and specifically includes in practice: intelligent comparing unit, for carrying out same type base between user
The competition of cause, i.e., to pass through the gene sequence of the gene order of the individual subscriber in account respective in gene library facilities and standard use-case
The comparison value of column is to compare with foundation, decided the winner by the height of score value, and showed that victor may be to the expression of the gene from score
Character development trend is bigger, is denoted as intelligent comparison result and records；
Health analysis module specifically includes: health analysis unit, for analyzing individual subscriber in the respective account of user
Gene order and the comparison result value of the gene order of the standard use-case of degree whole under corresponding classification, the mesh of comparison result value
Be analyze user individual subscriber gene order it is whether similar with certain inferior health, if similar, be denoted as A, and generate mesh
Preceding individual subscriber physical condition will reach time t required for this inferior health program1It is logical with possibility μ and this inferior health
Normal treatment time t2, according to different user characteristics similar A, t1And t2Mapped with this inferior health, mapping is public
Formula f (A) are as follows:
To obtain the potential sound development trend that user is determined by a certain type gene, and will potentially develop in a healthy way
Trend result returns；
Health analysis module health analysis unit analysis individual subscriber gene order under corresponding classification whole degree
Standard use-case gene order comparison result value, obtain user by the type it is gene-determined it is potential develop in a healthy way become
Gesture；The angle pin of guiding opinion unit profession provides reasonable healthy living guidance and daily life suggestion to the result.
Embodiment 2: as shown in Figure 1, a kind of interest health analysis device based on sequence alignment, including gene pool service
Device, the gene order for gene order and individual subscriber by different classes of, different degrees of storage standard use-case；
Sequence alignment module, for by the gene order of individual subscriber and the gene order of the standard use-case of corresponding classification into
Row similarity compares, and returns to the similarity value with the gene order of the standard use-case of each degree；
Intelligence compares with module, and the gene order for the same category between user is similar to the gene order of standard use-case
Degree compares with；
Health analysis module, for the gene order of a certain classification by analysis user and the gene order of standard use-case
The similarity of gene order under in various degree, obtains the development trend of user health, and provides health guidance and daily life
It is living to suggest.
Technology user will store equipment by gene and select a certain number of enough marks according to different inferior healths first
Mutatis mutandis example patient groups extract blood sample, carry out gene sequencing.The gene order that will be obtained, according to different inferior health, different
Performance degree uploads in gene pool server.User be derived from oneself blood sample sequencing gene, and by the gene order of oneself according to
Corresponding classification uploads in the gene pool of oneself.
Gene order comparison module is by the gene order each degree standard classified corresponding to gene pool that user uploads
Gene order is compared to generate using intelligent aligned sequences and is compared.There are multiple performance degree under the inferior health of a certain classification, often
Have multiple gene orders under a performance degree, each gene order is compared with user's gene order, each performance degree it is more
A similarity result acquires average value, and the average value of each performance degree acquires respectively shared ratio using calculating, obtains
The probability of each performance degree is counted as final result, and is stored in the database of user.
User can carry out intelligence with good friend and compare competition, and the gene comparison result of the same category of two users compares
Compared with, obtain victory or defeat, with intelligent comparison result prompt with open arms the potential illness of gene of user probability height, cause user itself
Attention.
The base of the gene order of health analysis module analysis individual subscriber and the standard use-case of degree whole under corresponding classification
Because of the comparison result value of sequence, user is obtained by the gene-determined potential sound development trend of the type, and with the angle of profession
Degree provides reasonable healthy living guidance and daily life suggestion for the result.
The invention has the advantages that can use that gene order caused by the analysis inferior health of advanced technology changes can
The development trend of energy property and user's body health, and reasonable Life Guidance and daily life suggestion are provided, it takes timely measure
Inferior health is prevented and treated, is benefited for society.
Claims (1)
1. a kind of gene sequencing device intelligently compared characterized by comprising
Gene pool server, according to the gene order of different classes of, different degrees of storage individual subscriber and the gene of standard use-case
Sequence；
Sequence alignment module, for by the gene of the gene order of the individual subscriber and the standard use-case of corresponding classification
Sequence carries out similarity comparison, and returns to the similarity value with the gene order of standard use-case；
Intelligence compares with module, and the gene order for the same category between user is similar to the gene order of the standard use-case
Degree compares with；
Health analysis module, gene order and the standard use-case for the individual subscriber by analyzing a certain classification
The similarity of gene order of the gene order under in various degree, obtains the development trend of user's inferior health, and provides health and refer to
It leads and daily life suggestion；
The gene pool server specifically includes: database storage unit, database control unit；
The database storage unit is led to for storing be mutually related " user ", " gene classification ", " performance degree " information
Reasonable database design is crossed, the gene order of the individual subscriber and " the performance degree " are joined with " the gene classification "
System contacts the gene order of the standard use-case, by the use with " the performance degree " with " the gene classification " respectively
The gene order of family individual and the gene order of the standard use-case are associated with " user "；Each user can only access certainly
Oneself gene pool cannot access the gene order of the individual subscriber of other users and standard use-case in gene pool server
Gene order；
The database control unit is added the database storage unit, modifies, delete operation；
The sequence alignment module includes: sequence alignment generation unit, gene order and the mark for the individual subscriber
Similarity comparison is carried out between the gene order of mutatis mutandis example, and is extracted and returned the result that the obtained similarity compares
Return, sequence alignment generate the following steps are included:
Step 1: the two sequences for participating in comparing are divided to obtain the feature vector of ten points to alphabet is carried out；
Step 2: by the desired value ki of the data of the feature vector of ten points, according to formula:
Wherein e is natural constant；
Pass through the desired value k of data of the formula to the feature vector of described ten pointsiIt is calculated, obtains and used with the standard
The desired value k of normal data of the gene order of examplepFeature it is poor, remember Δ ki, and according to described
The average data of the gene order of individual subscriber it is expected kaveThe i-th point of value formation sequence score information；
Pass through the obtained aiCreate scoring matrix；
Step 3: being given a mark according to the obtained scoring matrix；
Step 4: to by step 3 obtain higher than certain threshold value the participation compare two sequences to carry out both ends extension；
Step 5: to by step 4 obtain higher than certain threshold value the participation compare two sequences to assessing, obtain
Last high score segment；
Counting statistics unit, for counting the high score segment obtained by the step 5, and according to the two sequences pair for participating in comparing
Length gauge calculate similarity value；
The intelligence compares with module and specifically includes:
Intelligent comparing unit, for carrying out the competition of same type gene between user, i.e., with the user in respective account
The comparison value of the gene order of personal gene order and the standard use-case is to compare with foundation,
It decided the winner by the height of score value, the expression character development trend for obtaining victor to the gene from score is bigger, is denoted as
Intelligent comparison result simultaneously records；
The health analysis module specifically includes:
Health analysis unit, for analyzed in the respective account of user the gene order of the individual subscriber under corresponding classification
The comparison result value of the gene order of the standard use-case of whole degree, the purpose of comparison result value are the described of analysis user
Whether the gene order of individual subscriber is similar with the gene order of certain inferior health, if similar, is denoted as A, and generate and use at present
Family individual's physical condition will reach time t1 required for this inferior health program and possibility μ, and this inferior health
Typically last for time t2, according to different user characteristics the similar A, the t1 and t2 and this inferior health carry out into
Row mapping, mapping equation f (A) are as follows:
To obtain the potential inferior health development trend that user is determined by a certain type gene, and by the potential inferior health
Development trend result returns；It, can will be described since the gene order of the individual subscriber is easy to produce variation by environmental Kuznets Curves
Mapping equation f (A) is to be stored in the circular linked list that can be inquired, for the matching of sequence table, in case of a people's gene
The abnormality of sequence just sends the result to guiding opinion unit；
The guiding opinion unit is instructed for what is obtained for health analysis unit as a result, providing reasonable healthy living,
And daily life suggestion.
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| CN106897580B (en) * | 2017-02-10 | 2019-03-01 | 华东师范大学 | The calculation method of semantic similarity between a kind of gene based on vector |
| CN108629149B (en) * | 2017-03-21 | 2023-04-07 | 达易特基因科技股份有限公司 | Gene detection platform method |
| CN107341367A (en) * | 2017-06-02 | 2017-11-10 | 中国疾病预防控制中心传染病预防控制所 | The multidimensional data methods of exhibiting and system of a kind of drug resistant gene data platform |
| CN112951331A (en) * | 2021-03-31 | 2021-06-11 | 南阳市第二人民医院 | Breast cancer susceptibility gene screening method |
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