CN102485904A - Method of mammal micro RNA gene prediction - Google Patents
Method of mammal micro RNA gene prediction Download PDFInfo
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- CN102485904A CN102485904A CN2010105720528A CN201010572052A CN102485904A CN 102485904 A CN102485904 A CN 102485904A CN 2010105720528 A CN2010105720528 A CN 2010105720528A CN 201010572052 A CN201010572052 A CN 201010572052A CN 102485904 A CN102485904 A CN 102485904A
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Abstract
According to the characteristics that mammal micro RNA gene precursor sequences have high cross-species conservatism, starting from known micro RNA sequences, the invention provides a feasible bioinformatics method of micro RNA gene identification based on homologous prediction. According to the, micro RNA genes can be directly locked for further biological experiment verification. The method comprises the following steps: step 1, acquiring known mammal micro RNA precursor hairpin loop sequences; step 2, acquiring genome sequences of unknown species; step 3, searching for homologous sequences of micro RNA in genome by local comparison; step 4, screening potential precursor sequences according to a certain standard; step 5, forming a secondary structure by using RNA structure folding software; step 6, calculating the free energy of the secondary structure, and screening qualified micro RNA precursors; and step 7, predicting mature bodies of micro RNA. Finally, the experiment verification of interested micro RNA can be directly carried out.
Description
Technical field
The invention belongs to biological technical field, relate to miRNA (microRNA) predictive genes aspect.
Background technology
The present invention is a kind of Mammals miRNA method for forecasting gene.Be applicable to the biomedical research or the fundamental biological knowledge research of miRNA.
MiRNA originates from the endogenous expression transcript, is the singlestranded RNA that is about 21～24 Nucleotide, and its characteristic feature is that precursor has hairpin structure.The miRNA approach starts from the initial transcript of a miRNA gene.The hair fastener ring of these 70～100 Nucleotide is finally become precursor by the rnase processing treatment in nuclear.Gone into kytoplasm by nuclear output protein transport afterwards, then in kytoplasm, be processed as the ripe body miRNA of 21～24 Nucleotide by second rnase.The miRNA in this stage can combine silencing complex.It can suppress the translation of its messenger RNA(mRNA) (mRNA) through combining with target gene 3 ' end non-translational region identification, or degraded target messenger RNA(mRNA).MiRNA plays important regulation in the expression of post-transcriptional level regulatory gene and in processes such as the propagation of cell, differentiation, apoptosis.
Research at present thinks that miRNA has the conservative property (generally having only the difference of 1～2 base) of height in the mammalian genes group.What have conservative property most is let-7 family, and it extensively is present in the monosymmetric organism, and its sequence is conservative property very.The conservative property of miRNA has important biological significance, and prompting is in different biological development processes, and miRNA has identical regulatory mechanism, also for biological early stage evolution homology certain foundation is provided simultaneously.Utilize the characteristics of high conservative property can from the genome of the unknown, dope the miRNA gene.
Summary of the invention
The present invention has the advantages that highly stride the species conservative property according to Mammals miRNA (microRNA) precursor sequence; From known miRNA sequence; Found a kind of bioinformatics method of feasible miRNA gene identification based on the homology prediction; Can directly lock, so that further biological experiment checking to the miRNA gene.Implementation step is following:
Step 1: obtain known mammiferous miRNA precursor hair fastener ring sequence.
Step 2: the genome sequence that obtains species to be predicted.
Step 3: utilize local comparison, seek the homologous sequence of miRNA in the genome.
Step 4: according to certain standard screening potential precursor sequence.Concrete standard: 1) comparison length is greater than 95%, and base unanimity degree is greater than 80%; 2) precursor meets the hair fastener ring structure, and stem's length is greater than 15 bases, and there are not many ring phenomenons in ring portion; 3) there is not mutating alkali yl in ripe body position.
Step 5: utilize the folding software of Yeast Nucleic Acid (RNA) secondary structure to generate secondary structure.
Step 6: calculate the secondary structure free energy, screen qualified miRNA precursor.
Step 7: the ripe body sequence of prediction miRNA.
Step 8: final, for interested miRNA, checking can directly experimentize.
The present invention has the advantages that highly stride the species conservative property according to Mammals miRNA (microRNA) precursor sequence; From known miRNA sequence; Found a kind of bioinformatics method of feasible miRNA gene identification based on the homology prediction; Can directly lock, so that further biological experiment checking to the miRNA gene.
Aspect novelty, it is characterized in that: our method utilizes the miRNA precursor sequence in the conservative characteristics of Mammals camber, utilizes the method prediction miRNA gene of homology comparison.It is more reliable to predict the outcome, and helps in full genome range, excavating the miRNA gene.
Description of drawings
Fig. 1: basic flow sheet of the present invention
Fig. 2: the precursor secondary structure of miRNA and the instance that predicts the outcome of ripe body sequence.
Fig. 3: the result who utilizes RT-PCR (inverse transcription polymerase chain reaction) technology that the miRNA gene of prediction is verified
Embodiment:
Be instance with primate-monkey below, do further explanation.
Step 1: obtain known mammiferous all miRNA precursor hair fastener ring sequences from NCBi (www.ncbi.nlm.nih.gov/) website.
Step 2: the genome sequence that obtains monkey from NCBi (www.ncbi.nlm.nih.gov/) website.
Step 3: utilize local comparison software Blastn (http://blast.ncbi.nlm.nih.gov/), seek the homologous sequence of miRNA in the genome.
Step 4: according to certain standard screening potential precursor sequence.Concrete standard: 1) comparison length is greater than 95%, and base unanimity degree is greater than 80%; 2) precursor meets the hair fastener ring structure, and stem's length is greater than 15 bases, and there are not many ring phenomenons in ring portion; 3) there is not mutating alkali yl in ripe body position.
Step 5: utilize RNAfold (http://www.tbi.univie.ac.at/RNA/) software to carry out preceding folded body, analyze the secondary structure of precursor.
Step 6: utilize RNAeval (http://www.tbi.univie.ac.at/RNA/) to calculate the secondary structure free energy, screen qualified miRNA precursor.
Step 7: the ripe body sequence of prediction miRNA.Figure of description 2 is seen in predicting the outcome of the precursor secondary structure of one of them miRNA and ripe body sequence.
Step 8: final, for interested miRNA, utilize RT-PCR (inverse transcription polymerase chain reaction) technology that the miRNA gene of prediction is verified.The checking result sees accompanying drawing 3, and the result shows that the miRNA gene of the method prediction that utilizes us is accurately and reliably
More than be the description of this invention and non-limiting, based on other embodiment of inventive concept, all among protection scope of the present invention.
Claims (1)
1. the bioinformatics method that can predict Mammals miRNA (microRNA) can directly lock to the miRNA gene
Step 1: obtain known mammiferous miRNA precursor hair fastener ring sequence;
Step 2: the genome sequence that obtains unknown species;
Step 3: utilize local comparison, seek the homologous sequence of miRNA in the genome;
Step 4: according to three standard screening potential precursor sequence: 1) comparison length is greater than 95%, and base unanimity degree is greater than 80%; 2) precursor meets the hair fastener ring structure, and stem's length is greater than 15 bases, and there are not many ring phenomenons in ring portion; 3) there is not mutating alkali yl in ripe body position.
Step 5: utilize the folding software of Yeast Nucleic Acid (RNA) secondary structure to generate secondary structure;
Step 6: calculate the secondary structure free energy, screen qualified miRNA (microRNA) precursor;
Step 7: the ripe body of prediction miRNA.
Step 8: utilize RT-PCR (inverse transcription polymerase chain reaction) technology that the miRNA gene of prediction is verified.
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| CN201010572052.8A CN102485904B (en) | 2010-12-03 | 2010-12-03 | Method of mammal micro RNA gene prediction |
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| CN201010572052.8A CN102485904B (en) | 2010-12-03 | 2010-12-03 | Method of mammal micro RNA gene prediction |
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Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN106460041A (en) * | 2014-03-25 | 2017-02-22 | 亚利桑那州立大学董事会 | Detection of high variability regions between protein sequence sets representing a binary phenotype |
| CN106755378A (en) * | 2016-12-13 | 2017-05-31 | 北京林业大学 | A kind of method in detection miRNA sources |
-
2010
- 2010-12-03 CN CN201010572052.8A patent/CN102485904B/en not_active Expired - Fee Related
Non-Patent Citations (2)
| Title |
|---|
| 张志明等: "用生物信息学挖掘玉米中的microRNAs及其靶基因", 《作物学报》 * |
| 盛熙晖: "应用文库构建法和生物信息学方法鉴定绵羊microRNA", 《中国博士学位论文全文数据库》 * |
Cited By (2)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN106460041A (en) * | 2014-03-25 | 2017-02-22 | 亚利桑那州立大学董事会 | Detection of high variability regions between protein sequence sets representing a binary phenotype |
| CN106755378A (en) * | 2016-12-13 | 2017-05-31 | 北京林业大学 | A kind of method in detection miRNA sources |
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| CN102485904B (en) | 2015-05-06 |
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