CN108875306A - A kind of method and system for searching Sex Determination sequence - Google Patents
A kind of method and system for searching Sex Determination sequence Download PDFInfo
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- CN108875306A CN108875306A CN201810551156.7A CN201810551156A CN108875306A CN 108875306 A CN108875306 A CN 108875306A CN 201810551156 A CN201810551156 A CN 201810551156A CN 108875306 A CN108875306 A CN 108875306A
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Abstract
The invention discloses a kind of method and system for searching Sex Determination sequence, the method for the lookup Sex Determination sequence includes：The sample of multiple females or male is sequenced, data is obtained, and genome will be referred on comparing, obtains comparison result, wherein include with reference to genome：The sequence of sex determinative chromosome Y or W；Comparison result is handled, the sequencing depth of each base is obtained；Genome on comparing is divided at least one window, and multiple females or male are calculated with the base coverage of each window at least one window；To each window, the average base coverage of multiple males or female sample is counted；According to average base coverage, the Sex Determination sequence of the sample of multiple females or male is determined.
Description
Technical field
The present invention relates to technical field of biological information, and in particular to it is a kind of based on search Sex Determination sequence method and be
System.
Background technique
Currently, the method for looking for Sex Determination sequence is CQ (chromosome quotient method) [1], it will be female
Sample and male sample compared on the genome of Sex Determination respectively, find the big region of coverage difference, then it is assumed that
It is Sex Determination sequence.For example the gender of the mankind is that chromosome is determined by Y, male XY, women XX.In order to find gender
Determining sequence (Y), the sequencing data of male and the sequencing data of women are compared upper male gene group by us, count every dyeing
The base coverage of body, it finds that there is item chromosome, in the comparison result of women, base coverage is very low (0.3),
And in the comparison result of male, base coverage is very high (0.98), then this chromosome is male sex chromosome Y.
But the species (such as diamondback moth) of big, the high heterozygosis of individual variation small for sex chromosome's difference, this method
It is just not applicable.
Summary of the invention
The purpose of the present invention is to provide a kind of method and system for searching Sex Determination sequence, to solve the prior art
The problem of.
To achieve the above object, the technical scheme is that a kind of method for searching Sex Determination sequence, feature exist
In, the method for the lookup Sex Determination sequence, including：The sample of multiple females or male is sequenced, data are obtained, and
Genome will be referred on comparing, obtain comparison result, wherein include with reference to genome：Sex determinative chromosome Y's or W
Sequence；Comparison result is handled, the sequencing depth of each base is obtained；Genome on comparing is divided at least one window
Mouthful, and multiple females or male are calculated with the base coverage of each window at least one window；To each window, system
Count the average base coverage of multiple males or female sample；According to average base coverage, determine multiple female or male
The Sex Determination sequence of sample.
Optionally, the sample of multiple females or male is sequenced, obtains data, and base will be referred on comparing
Because of group, comparison result is obtained, including：The sample of multiple females or male is sequenced by Illumina platform, obtains number
According to, and data BWA software is compared and refers to genome, obtain comparison result.
Optionally, comparison result is handled, the sequencing depth of each base is obtained, including：It is handled using SAMtools software
Comparison result obtains the sequencing depth of each base.
Optionally, the base coverage of each window at least one window is calculated, including：It will be sequenced in each window
Base number of the depth greater than 0 is counted, then divided by the length of each window.
Optionally, according to average base coverage, the Sex Determination sequence of the sample of multiple females or male, packet are determined
It includes：When reference genome includes：The sequence of sex determinative chromosome Y, and determine the average base covering of multiple female samples
Degree is greater than 70%, and when the average base coverage of multiple female samples is less than 10%, is determined as female sex's determining sequence；Or
Person, when reference genome includes：The sequence of sex determinative chromosome W, and determine the average base covering of multiple female samples
Degree is greater than 70%, and when the average base coverage of multiple male samples is less than 10%, is determined as female sex's determining sequence.
To achieve the above object, the technical scheme is that a kind of system for searching Sex Determination sequence, the lookup
The system of other determining sequence, including：Unit, comparing unit, processing unit, computing unit, statistic unit and determination unit is sequenced；
Wherein, unit is sequenced, for the sample of multiple females or male to be sequenced, obtains data；Comparing unit is used for data
Genome is referred in comparison, obtains comparison result, wherein include with reference to genome：The sequence of sex determinative chromosome Y or W；Place
It manages unit and obtains the sequencing depth of each base for handling comparison result；Computing unit, for by the base on comparing
Because group is divided at least one window, and the base for calculating each window at least one window to multiple females or male is covered
Cover degree；Statistic unit, for counting the average base coverage of multiple males or female sample to each window；Determination unit,
For determining the Sex Determination sequence of the sample of multiple females or male according to average base coverage.
Optionally, unit is sequenced, is specifically used for：The sample of multiple females or male is surveyed by Illumina platform
Sequence obtains data；Comparing unit is specifically used for：Data BWA software is compared and refers to genome, obtains comparison result.
Optionally, processing unit is specifically used for：Comparison result is handled using SAMtools software, obtains each base
Depth is sequenced.
Optionally, computing unit is specifically used for：Base number of the depth greater than 0 will be sequenced in each window to count,
Again divided by the length of each window.
Optionally, determination unit is specifically used for：Include with reference to genome when described：The sequence of sex determinative chromosome Y,
And determine that the average base coverage of the multiple female sample is greater than 70%, and the average base of the multiple female sample
When coverage is less than 10%, it is determined as female sex's determining sequence；Alternatively, including with reference to genome when described：Sex Determination dye
The sequence of colour solid W, and determine that the average base coverage of the multiple female sample is greater than 70%, and the multiple male sample
When the average base coverage of product is less than 10%, it is determined as female sex's determining sequence.
The invention has the advantages that：
Whole sequence is cut into small window to analyze, compared with the prior art in chromosome difference hour, it is right
Whole sequence is analyzed, and the Sex Determination sequence in whole sequence can be more accurately found.
Detailed description of the invention
Fig. 1 is that the embodiment of the invention provides a kind of flow charts of method for searching Sex Determination sequence.
Fig. 2 is that the embodiment of the invention provides a kind of structural schematic diagrams of system for searching Sex Determination sequence.
Specific embodiment
The following examples are used to illustrate the present invention, but are not intended to limit the scope of the present invention..
Embodiment 1
Fig. 1 is that the embodiment of the invention provides a kind of flow charts of method for searching Sex Determination sequence.As shown in Figure 1,
The method of the lookup Sex Determination sequence includes the following steps：
Step S101：The sample of multiple females or male is sequenced, obtains data, and will refer on comparing
Genome obtains comparison result, wherein include with reference to genome：The sequence of sex determinative chromosome Y or W；
Specifically, the sample of multiple females or male is sequenced by Illumina platform, obtains data, and will
Data BWA software, which compares, refers to genome, obtains comparison result.
It should be noted that sequencing approach includes but is not limited to Illumina platform, by data and genome alignment is referred to
On method include but is not limited to BWA.
In embodiments of the present invention, use female diamondback moth as with reference to genome (ZW, female determine gender), survey respectively
It is (each to have found 10,453 windows by searching for the method for Sex Determination sequence for 50 males and 50 female individuals
Window 30bp).
Step S102：Comparison result is handled, the sequencing depth of each base is obtained；
Specifically, comparison result is handled using SAMtools software, obtains the sequencing depth of each base.
Step S103：Genome on comparing is divided at least one window, and multiple females or male are counted
Calculate the base coverage of each window at least one window；
Specifically, base number of the depth greater than 0 will be sequenced in each window to count, then divided by the length of each window
Degree.
For example, each window can be dimensioned to 50bp, each window can also be sized to difference
's.
Step S104：To each window, the average base coverage of multiple males or female sample is counted；
Step S105：According to average base coverage, the Sex Determination sequence of the sample of multiple females or male is determined.
Specifically, when reference genome includes：The sequence of sex determinative chromosome Y, and determine multiple female samples
Average base coverage is greater than 70%, and when the average base coverage of multiple female samples is less than 10%, is determined as female
Other determining sequence；Alternatively, when including with reference to genome：The sequence of sex determinative chromosome W, and determine multiple female samples
Average base coverage is greater than 70%, and when the average base coverage of multiple male samples is less than 10%, is determined as female
Other determining sequence.
Embodiment 2
Fig. 2 is that the embodiment of the invention provides a kind of systems for searching Sex Determination sequence.As shown in Fig. 2, the lookup
The system of other determining sequence, including：Unit 21, comparing unit 22, processing unit 23, computing unit 24, statistic unit 25 is sequenced
With determination unit 26；Wherein,
Unit 21 is sequenced, for the sample of multiple females or male to be sequenced, obtains data；Comparing unit 22 is used
In genome will be referred on comparing, comparison result is obtained, wherein include with reference to genome：Sex determinative chromosome Y or W
Sequence；Processing unit 23 obtains the sequencing depth of each base for handling comparison result；Computing unit 24, for that will count
It is divided at least one window according to the genome in comparison, and multiple females or male is calculated each at least one window
The base coverage of window；Statistic unit 25, for each window, the average base for counting multiple males or female sample to cover
Cover degree；Determination unit 26, for determining the Sex Determination sequence of the sample of multiple females or male according to average base coverage
Column.
Optionally, unit 21 is sequenced, is specifically used for：The sample of multiple females or male is carried out by Illumina platform
Sequencing obtains data.
Optionally, comparing unit 22 are specifically used for：Data BWA software is compared and refers to genome, obtains and compares knot
Fruit.
Optionally, processing unit 23 are specifically used for：Comparison result is handled using SAMtools software, obtains each base
Sequencing depth.
Optionally, computing unit 24 are specifically used for：
Base number of the depth greater than 0 will be sequenced in each window to count, then divided by the length of each window.
Optionally, determination unit 26 are specifically used for：When reference genome includes：The sequence of sex determinative chromosome Y, with
And determine that the average base coverage of multiple female samples is greater than 70%, and the average base coverage of multiple female samples is less than
When 10%, it is determined as female sex's determining sequence；Alternatively, when including with reference to genome：The sequence of sex determinative chromosome W, with
And determine that the average base coverage of multiple female samples is greater than 70%, and the average base coverage of multiple male samples is less than
When 10%, it is determined as female sex's determining sequence.The description of 26 part of determination unit can be detailed in the description of the part step S105.
The embodiment of the present invention is analyzed by the way that whole sequence is cut into small window, compared with the prior art in
Chromosome difference hour, whole sequence is analyzed, can more accurately find the Sex Determination sequence in whole sequence.
Although above having used general explanation and specific embodiment, the present invention is described in detail, at this
On the basis of invention, it can be made some modifications or improvements, this will be apparent to those skilled in the art.Therefore,
These modifications or improvements without departing from theon the basis of the spirit of the present invention are fallen within the scope of the claimed invention.
Claims (10)
1. a kind of method for searching Sex Determination sequence, which is characterized in that the method, including：
The sample of multiple females or male is sequenced, data is obtained, and genome will be referred on the comparing, obtains
Obtain comparison result, wherein described to include with reference to genome：The sequence of sex determinative chromosome Y or W；
The comparison result is handled, the sequencing depth of each base is obtained；
Genome on the comparing is divided at least one window, and to described in the multiple female or male calculating
The base coverage of each window at least one window；
To each window, the average base coverage of the multiple male or female sample is counted；
According to the average base coverage, the Sex Determination sequence of the sample of the multiple female or male is determined.
2. the method according to claim 1, wherein it is described by it is multiple female or male sample be sequenced,
Data are obtained, and genome will be referred on the comparing, obtain comparison result, including：
The sample of multiple females or male is sequenced by Illumina platform, obtains data, and the data are used
BWA software compares and refers to genome, obtains comparison result.
3. the method according to claim 1, wherein the processing comparison result, obtains each base
Depth is sequenced, including：
The comparison result is handled using SAMtools software, obtains the sequencing depth of each base.
4. the method according to claim 1, wherein each window at least one window described in the calculating
Base coverage, including：
Base number of the depth greater than 0 will be sequenced in each window to count, then divided by the length of each window.
5. the method according to claim 1, wherein described according to the average base coverage, determine described in
The Sex Determination sequence of the sample of multiple females or male, including：
Include with reference to genome when described：The sequence of sex determinative chromosome Y, and determine being averaged for the multiple female sample
Base coverage is greater than 70%, and when the average base coverage of the multiple female sample is less than 10%, is determined as female
Other determining sequence；Alternatively,
Include with reference to genome when described：The sequence of sex determinative chromosome W, and determine being averaged for the multiple female sample
Base coverage is greater than 70%, and when the average base coverage of the multiple male sample is less than 10%, is determined as female
Other determining sequence.
6. a kind of system for searching Sex Determination sequence, which is characterized in that the system, including：Be sequenced unit, comparing unit,
Processing unit, computing unit, statistic unit and determination unit；Wherein,
The sequencing unit obtains data for the sample of multiple females or male to be sequenced；
The comparing unit obtains comparison result for will refer to genome on the comparing, wherein described to refer to base
Because group includes：The sequence of sex determinative chromosome Y or W；
The processing unit obtains the sequencing depth of each base for handling the comparison result；
The computing unit, for the genome on the comparing to be divided at least one window, and to the multiple
Female or male calculate the base coverage of each window at least one described window；
The statistic unit, for counting the average base covering of the multiple male or female sample to each window
Degree；
The determination unit, for determining the property of the sample of the multiple female or male according to the average base coverage
Other determining sequence.
7. system according to claim 6, which is characterized in that the sequencing unit is specifically used for：By multiple females or hero
Property sample be sequenced by Illumina platform, obtain data；
The comparing unit, is specifically used for：Data BWA software is compared and refers to genome, obtains comparison result.
8. system according to claim 6, which is characterized in that the processing unit is specifically used for：
The comparison result is handled using SAMtools software, obtains the sequencing depth of each base.
9. system according to claim 6, which is characterized in that the computing unit is specifically used for：
Base number of the depth greater than 0 will be sequenced in each window to count, then divided by the length of each window.
10. the method according to claim 1, wherein the determination unit, is specifically used for：
Include with reference to genome when described：The sequence of sex determinative chromosome Y, and determine being averaged for the multiple female sample
Base coverage is greater than 70%, and when the average base coverage of the multiple female sample is less than 10%, is determined as female
Other determining sequence；Alternatively,
Include with reference to genome when described：The sequence of sex determinative chromosome W, and determine being averaged for the multiple female sample
Base coverage is greater than 70%, and when the average base coverage of the multiple male sample is less than 10%, is determined as female
Other determining sequence.
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| CN103805689A (en) * | 2012-11-15 | 2014-05-21 | 深圳华大基因科技服务有限公司 | Characteristic kmer based metatypic chromosomal sequence assembly method and application thereof |
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Application publication date: 20181123 |