CN101717822A - RNA sequence secondary structure prediction method based on base fragment coding and ant colony optimization - Google Patents
RNA sequence secondary structure prediction method based on base fragment coding and ant colony optimization Download PDFInfo
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- CN101717822A CN101717822A CN200910218023A CN200910218023A CN101717822A CN 101717822 A CN101717822 A CN 101717822A CN 200910218023 A CN200910218023 A CN 200910218023A CN 200910218023 A CN200910218023 A CN 200910218023A CN 101717822 A CN101717822 A CN 101717822A
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Abstract
The invention relates to a RNA sequence secondary structure prediction method based on base fragment coding and ant colony optimization, belonging to the field of bioinformatics research. The RNA sequence secondary structure prediction method comprises the steps of: recoding an RNA sequence, and obtaining a corresponding coding sequence according to corresponding values in a coding table and a coding association list; eliminating a redundancy stem region by a strategy of extending rightwards according to an exact matching table and a partial matching table to obtain all possible useable stem region sets; giving two-dimensional heuristic information in the ant colony optimization, selection rule of an initial stem region and the next stem region and updating strategy of pheromones to construct compatible subsets of all possible stem region sets; and finally obtaining a secondary structure with minimum free energy. The invention can rapidly, accurately and effectively predict the secondary structure without including a pseudojnot RNA sequence, can output the obtained result in a bracket mode way, and is superior to the main prediction technology at present in the aspects of sensitivity and specificity of the prediction of the RNA sequence second structure.
Description
Technical field
The invention belongs to the information biology research field.
Background technology
Studies show that RNA has played important effect in gene regulating, and the function of RNA and structure are closely-related, therefore the functional performance of wanting to understand the RNA sequence should be started with from its structure earlier.Obtained at present a large amount of RNA sequence primary structure information, increasing researchist begins to pay close attention to the secondary structure and the tertiary structure of RNA sequence, but determine that with the method for Bioexperiment its tertiary structure cost is high, difficulty is big, and is not all effective to all molecules.The tertiary structure of RNA sequence is difficult to directly obtain by primary structure simultaneously, and directly at the theoretical prediction of its tertiary structure, progress is not very smooth, and the prediction secondary structure is to obtain the only way which must be passed of tertiary structure.Therefore by the secondary structure of software simulation with prediction RNA sequence, and combine with embedded system based on the ARM system, form embedded RNA sequence secondary structure prediction method, with lower cost and faster the time obtain to have certain confidence level result's mode, become the important means of information biology.
Summary of the invention
The object of the present invention is to provide a kind of can be fast, prediction does not comprise false knot accurately and efficiently RNA sequence secondary structure, and with the method for gained result with the output of bracket method pattern.
The present invention includes the following step:
1. carry out the pre-treatment of RNA sequence, specifically comprise the following steps:
1) with RNA sequence input CPLD.
2) by the coding contingency table with the RNA sequence with the coding form be stored among the SRAM, the coding contingency table be present in the system, but and real-time calling, it is converted to the figure pattern that is easy to systems analysis with the RNA sequence of being obtained.
2. carry out RNA sequence secondary structure prediction, specifically comprise the following steps:
1) obtain the stem district set that length is n according to matching list, matching list is present in the system, but and real-time calling, it is with switched RNA sequence information, being combined as length is the stem district set of n.
2) be that the stem district of n adopts the strategy that extends to the right to all length, obtain the stem district set of all length greater than n; The strategy of Yan Shening can calculate the stem district set of all length greater than n to the right.
3) will draw corresponding to the set of all possible stem district of RNA sequence, be stored in and wait among the SDRAM and calling;
4) utilize a certain stem of ARM control chip picked at random district, as the initial node of ant group algorithm;
5) utilize next stem district of policy selection of roulette, up to the set of selectable stem district for empty;
6) minimum free energy of every corresponding secondary structure of ant of calculating, the secondary structure of record and renewal energy minimum;
7), and choose initial node once more and carry out loop computation according to the pheromone value between the given Policy Updates stem district;
8) reach given iteration step number or the satisfied condition that circulates and withdraw from, the secondary structure of exporting the RNA sequence with the bracket method pattern is to LCD, and the iteration step number can be provided with in system in advance.
The present invention can effectively simulate and predict the RNA sequence secondary structure that does not comprise false knot.The present invention carries out recompile by the base sequence with typing, and then obtain corresponding coding sequence by the respective value of coding in the contingency table, and according to complete matching list and incomplete matching list, reject redundant stem district by extension function to the right, obtain the set of all possible useful stem district, according to the selection rule and the pheromone update strategy in the heuristic information of two dimension in the ant group algorithm, initial stem district and next stem district, construct the compatible subclass of all possible stem district set then.
The present invention uses concurrent technique that the secondary structure of RNA sequence is predicted more fast and accurately, can access the compatible stem district set of free energy minimum, the present invention can also test and analyze the sequence of picked at random in the international public database, and the gained result can be exported with the bracket method pattern, make structure representation more directly perceived accurately, experimental result shows that the present invention all is being better than present main flow forecasting techniques aspect susceptibility and the specificity.
Description of drawings
Fig. 1 is the RNA sequence secondary structure prediction method flow diagram based on base fragment coding and ant group algorithm
Fig. 2 is the RNA sequence secondary structure prediction system architecture synoptic diagram based on base fragment coding and ant group algorithm
Embodiment
The present invention is a kind of RNA sequence secondary structure prediction method based on base fragment coding and ant group algorithm, as shown in Figure 1, with gained RNA sequence input CPLD, by the coding contingency table RNA sequence is encoded, the RNA sequence is stored among the SRAM with the form of encoding sequence, and obtain the stem district set that length is n according to matching list, to all length is that the stem district of n adopts the strategy that extends to obtain the stem district set of all length greater than n to the right, being stored in corresponding to the set of all possible stem district of RNA sequence of drawing waited among the SDRAM and being called, then by the initial node of a certain stem of ARM control chip picked at random district as ant group algorithm, and utilize next stem district of policy selection of roulette, be sky until the set of selectable stem district, calculate the minimum free energy of every corresponding secondary structure of ant at last, the secondary structure of record and renewal energy minimum, according to the pheromone value between the given Policy Updates stem district, and choose initial node once more and carry out loop computation, until reaching given iteration step number or satisfying the condition that circulation is withdrawed from, export RNA sequence secondary structure in LCD with the pattern of bracket method.
Claims (7)
1. the RNA sequence secondary structure prediction method based on base fragment coding and ant group algorithm is characterized in that comprising the following steps:
1) carries out the pre-treatment of RNA sequence;
2) carry out RNA sequence secondary structure prediction.
2. by the described RNA sequence secondary structure prediction method of claim 1, it is characterized in that the pre-treatment of the described RNA sequence of step 1) comprises the following steps: based on base fragment coding and ant group algorithm
1) with RNA sequence input CPLD;
2) by the coding contingency table form of RNA sequence with coding is stored among the SRAM.
3. by the described RNA sequence secondary structure prediction method of claim 1, it is characterized in that step 2 based on base fragment coding and ant group algorithm) described RNA sequence secondary structure prediction comprises the following steps:
1) obtains the stem district set that length is n according to matching list;
2) be that the stem district of n adopts the strategy that extends to the right to all length, obtain the stem district set of all length greater than n;
3) will draw corresponding to the set of all possible stem district of RNA sequence, be stored in and wait among the SDRAM and calling;
4) utilize a certain stem of ARM control chip picked at random district, as the initial node of ant group algorithm;
5) utilize next stem district of policy selection of roulette, up to the set of selectable stem district for empty;
6) minimum free energy of every corresponding secondary structure of ant of calculating, the secondary structure of record and renewal energy minimum;
7), and choose initial node once more and carry out loop computation according to the pheromone value between the given Policy Updates stem district;
8) reach given iteration step number or the satisfied condition that circulates and withdraw from, the secondary structure of exporting the RNA sequence with the bracket method pattern is to LCD.
4. by the described RNA sequence secondary structure prediction method of claim 2 based on base fragment coding and ant group algorithm, it is characterized in that step 2) described coding contingency table is present in the system, but and real-time calling, it is converted to the figure pattern that is easy to systems analysis with the RNA sequence of being obtained.
5. by the described RNA sequence secondary structure prediction method of claim 3 based on base fragment coding and ant group algorithm, it is characterized in that the described matching list of step 1) is present in the system, but and real-time calling, it is switched RNA sequence information, being combined as length is the stem district set of n.
6. by the described RNA sequence secondary structure prediction method of claim 3, it is characterized in that step 2 based on base fragment coding and ant group algorithm) the described strategy that extends to the right, can calculate the stem district set of all length greater than n.
7. by the described RNA sequence secondary structure prediction method of claim 3, it is characterized in that the described iteration step number of step 8) can be provided with in advance in system based on base fragment coding and ant group algorithm.
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Cited By (7)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN102880811A (en) * | 2012-10-24 | 2013-01-16 | 吉林大学 | Method for predicting secondary structure of ribonucleic acid (RNA) sequence based on complex programmable logic device (CPLD) base fragment encoding and ant colony algorithm |
| CN103235902A (en) * | 2013-04-18 | 2013-08-07 | 山东建筑大学 | Prediction method for ribose nucleic acid (RNA) structure comprising false knots |
| CN103593587A (en) * | 2013-11-20 | 2014-02-19 | 吉林大学 | Component-based identification method and device of long-chain RNA secondary structures with pseudo knots |
| CN109273047A (en) * | 2017-12-15 | 2019-01-25 | 武汉科技大学 | A kind of nucleic acid structure prediction technique based on simulated annealing |
| CN109599146A (en) * | 2018-11-08 | 2019-04-09 | 武汉科技大学 | A kind of band false knot nucleic acid Structure Prediction Methods based on multi-objective genetic algorithm |
| CN117116361A (en) * | 2023-10-25 | 2023-11-24 | 江西师范大学 | 12sRNA secondary structure visualization method based on fixed frame |
| CN117497092A (en) * | 2024-01-02 | 2024-02-02 | 合肥微观纪元数字科技有限公司 | RNA structure prediction method and system based on dynamic programming and quantum annealing |
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2009
- 2009-12-16 CN CN200910218023A patent/CN101717822A/en active Pending
Cited By (12)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN102880811A (en) * | 2012-10-24 | 2013-01-16 | 吉林大学 | Method for predicting secondary structure of ribonucleic acid (RNA) sequence based on complex programmable logic device (CPLD) base fragment encoding and ant colony algorithm |
| CN103235902A (en) * | 2013-04-18 | 2013-08-07 | 山东建筑大学 | Prediction method for ribose nucleic acid (RNA) structure comprising false knots |
| CN103235902B (en) * | 2013-04-18 | 2016-03-09 | 山东建筑大学 | Comprise the RNA Structure Prediction Methods of false knot |
| CN103593587A (en) * | 2013-11-20 | 2014-02-19 | 吉林大学 | Component-based identification method and device of long-chain RNA secondary structures with pseudo knots |
| CN109273047A (en) * | 2017-12-15 | 2019-01-25 | 武汉科技大学 | A kind of nucleic acid structure prediction technique based on simulated annealing |
| CN109273047B (en) * | 2017-12-15 | 2022-09-16 | 武汉科技大学 | Nucleic acid structure prediction method based on simulated annealing |
| CN109599146A (en) * | 2018-11-08 | 2019-04-09 | 武汉科技大学 | A kind of band false knot nucleic acid Structure Prediction Methods based on multi-objective genetic algorithm |
| CN109599146B (en) * | 2018-11-08 | 2022-04-15 | 武汉科技大学 | Multi-target genetic algorithm-based nucleic acid structure prediction method with false knots |
| CN117116361A (en) * | 2023-10-25 | 2023-11-24 | 江西师范大学 | 12sRNA secondary structure visualization method based on fixed frame |
| CN117116361B (en) * | 2023-10-25 | 2024-01-26 | 江西师范大学 | 12sRNA secondary structure visualization method based on fixed frame |
| CN117497092A (en) * | 2024-01-02 | 2024-02-02 | 合肥微观纪元数字科技有限公司 | RNA structure prediction method and system based on dynamic programming and quantum annealing |
| CN117497092B (en) * | 2024-01-02 | 2024-05-14 | 微观纪元(合肥)量子科技有限公司 | RNA structure prediction method and system based on dynamic programming and quantum annealing |
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