CN102880811A - Method for predicting secondary structure of ribonucleic acid (RNA) sequence based on complex programmable logic device (CPLD) base fragment encoding and ant colony algorithm - Google Patents
Method for predicting secondary structure of ribonucleic acid (RNA) sequence based on complex programmable logic device (CPLD) base fragment encoding and ant colony algorithm Download PDFInfo
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- CN102880811A CN102880811A CN2012104074908A CN201210407490A CN102880811A CN 102880811 A CN102880811 A CN 102880811A CN 2012104074908 A CN2012104074908 A CN 2012104074908A CN 201210407490 A CN201210407490 A CN 201210407490A CN 102880811 A CN102880811 A CN 102880811A
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Abstract
The invention discloses a method for predicting a secondary structure of a ribonucleic acid (RNA) sequence based on complex programmable logic device (CPLD) base fragment encoding and ant colony algorithm and belongs to the field of bioinformatics research. The method comprises the following steps: recoding the RNA sequence according to an association table by using the CPLD; obtaining a corresponding encoding sequence according to corresponding value in an encoding table and an encoded association table, removing a redundancy stem area through a right extension strategy through a complete matching table and an incomplete matching table, and obtaining all possible stem area sets; giving two-dimensional heuristic information and a selection rule of an initial stem area and the next stem area in the ant colony algorithm, and constructing a compatible subset of all the possible stem area sets through an information element update strategy; and finally, obtaining the secondary structure with the minimum free energy. The method can rapidly, accurately and effectively predict the secondary structure of the RNA sequence which does not contain false knots and output the obtained result in a bracketing mode, has sensitivity and specificity in the aspect of judging two parameters for predicting the advantages and weakness of the secondary structure of the RNA sequence, and is superior to the conventional mainstream prediction technology.
Description
Technical field
The invention belongs to the bioinformatics research field.
Background technology
Studies show that, RNA has played very important effect in gene regulation, and the function of RNA and structure are closely-related, and the functional characteristic of therefore wanting to understand the RNA sequence should be started with from its structure first.Obtained at present a large amount of RNA sequence primary structure information, but the useful information that primary structure comprises is fewer, therefore increasing researchist begins to pay close attention to secondary structure and the tertiary structure of RNA sequence, but the tertiary structure cost of determining RNA with the method for Bioexperiment is high, difficulty is large, and the method is not all effective to all molecules.Because the tertiary structure of RNA sequence is difficult to directly obtain by primary structure, and directly towards the theoretical prediction of tertiary structure, progress neither be very smooth, therefore predicts that secondary structure is to obtain the only way which must be passed of tertiary structure.Therefore the RNA secondary structure that software simulation and prediction is obtained, with be combined based on the embedded system of ARM system, formation is based on Embedded RNA sequence secondary structure prediction method, thereby can obtain the mode that a kind of low cost, high-level efficiency and result have certain confidence level, become the important means of bioinformatics.
Summary of the invention
The object of the present invention is to provide and a kind ofly can predict fast, accurately and efficiently RNA sequence secondary structure (not containing false knot) and with the method for acquired results with bracket method pattern output.The needed hardware device of the method comprise processor, internal memory, mainboard,
The present invention includes the following step:
1.RNA the pre-service of sequence specifically comprises the following steps:
1) with RNA sequence input CPLD.
2) CPLD 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 systematic analysis with the RNA sequence of obtaining.
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 all length greater than the stem district set of n; Use the strategy that extends to the right, can calculate all length greater than the stem district set of 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 the ARM control chip to choose at random a certain stem district, as the initial node of ant group algorithm;
5) utilize next stem district of roulette policy selection, until the set of selectable stem district is 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) according to the pheromones value between the given Policy Updates stem district, and again choose initial node and carry out loop computation;
8) reach given iterative steps or satisfy the condition that circulation is withdrawed from, the secondary structure of RNA sequence is outputed to LCD with the bracket method pattern, iterative steps can be set in system in advance.
The present invention can simulate effectively and predict that the RNA sequence does not contain the secondary structure of false knot.The present invention at first carries out recompile with the base sequence of typing, and then obtain corresponding coded sequence by the respective value of coding in the contingency table, and according to complete matching list and Incomplete matching table, by extension function eliminate redundancy stem district to the right, obtain all possible stem district set that satisfies condition, then according to selection rule and the pheromones update strategy in two-dimentional heuristic information, initial stem district and next stem district in the ant group algorithm, construct the compatible subset of all possible stem district set.
The present invention uses concurrent technique with the secondary structure of RNA sequence with more fast and accurately prediction out, can access the compatible stem district set of free energy minimization, the present invention can also test and analyze the sequence of choosing at random in the international public database, and acquired results 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 CPLD base fragment coding and ant group algorithm
Fig. 2 is the RNA sequence secondary structure prediction system architecture schematic diagram based on CPLD base fragment coding and ant group algorithm
Embodiment
The present invention is a kind of RNA sequence secondary structure prediction method based on CPLD 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 coded sequence, and obtain the stem district set that length is n according to matching list, be that the stem district of n adopts the strategy that extends to obtain all length greater than the stem district set of n to the right to all length, 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 choose at random a certain stem district as the initial node of ant group algorithm by the ARM control chip, and utilize next stem district of policy selection of roulette, until the set of selectable stem district is for empty, calculate at last the minimum free energy of every corresponding secondary structure of ant, the secondary structure of record and renewal energy minimum, according to the pheromones value between the given Policy Updates stem district, and again choose initial node and carry out loop computation, until reach given iterative steps or satisfy 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 CPLD base fragment coding and ant group algorithm is characterized in that comprising the following steps:
1) carries out the pre-service of RNA sequence;
2) carry out RNA sequence secondary structure prediction.
2. by the RNA sequence secondary structure prediction method based on base fragment coding and ant group algorithm claimed in claim 1, it is characterized in that step 1) pre-service of described RNA sequence comprises the following steps:
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 RNA sequence secondary structure prediction method based on base fragment coding and ant group algorithm claimed in claim 1, it is characterized in that step 2) 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 all length greater than the stem district set of 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 the ARM control chip to choose at random a certain stem district, as the initial node of ant group algorithm;
5) utilize next stem district of policy selection of roulette, until the set of selectable stem district is 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) according to the pheromones value between the given Policy Updates stem district, and again choose initial node and carry out loop computation;
8) reach given iterative steps or the satisfied condition that circulates and withdraw from, export the secondary structure of RNA sequence with the bracket method pattern to LCD.
4. by the RNA sequence secondary structure prediction method based on base fragment coding and ant group algorithm claimed in claim 2, 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 systematic analysis with the RNA sequence of obtaining.
5. by the RNA sequence secondary structure prediction method based on base fragment coding and ant group algorithm claimed in claim 3, it is characterized in that step 1) described matching list 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 RNA sequence secondary structure prediction method based on base fragment coding and ant group algorithm claimed in claim 3, it is characterized in that step 2) the described strategy that extends to the right, can calculate all length greater than the stem district set of n.
7. by the RNA sequence secondary structure prediction method based on base fragment coding and ant group algorithm claimed in claim 3, it is characterized in that step 8) described iterative steps can arrange in system in advance.
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Cited By (4)
| Publication number | Priority date | Publication date | Assignee | Title |
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| 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 |
| CN107577922A (en) * | 2017-09-20 | 2018-01-12 | 吉林大学 | A kind of corn lncRNA sifting sort methods based on arm processor |
| 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 |
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| US20060031026A1 (en) * | 2004-08-09 | 2006-02-09 | Inha-Industry Partnership | Method and system for extracting and visualizing secondary RNA structure elements from protein-RNA complexes |
| CN101717822A (en) * | 2009-12-16 | 2010-06-02 | 吉林大学 | RNA sequence secondary structure prediction method based on base fragment coding and ant colony optimization |
| CN101908102A (en) * | 2010-08-13 | 2010-12-08 | 山东建筑大学 | Ribosomal stalk based predicting method and device of RNA (Ribonucleic Acid) secondary structure |
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Patent Citations (3)
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| US20060031026A1 (en) * | 2004-08-09 | 2006-02-09 | Inha-Industry Partnership | Method and system for extracting and visualizing secondary RNA structure elements from protein-RNA complexes |
| CN101717822A (en) * | 2009-12-16 | 2010-06-02 | 吉林大学 | RNA sequence secondary structure prediction method based on base fragment coding and ant colony optimization |
| CN101908102A (en) * | 2010-08-13 | 2010-12-08 | 山东建筑大学 | Ribosomal stalk based predicting method and device of RNA (Ribonucleic Acid) secondary structure |
Cited By (8)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| 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 |
| CN107577922A (en) * | 2017-09-20 | 2018-01-12 | 吉林大学 | A kind of corn lncRNA sifting sort methods based on arm processor |
| CN107577922B (en) * | 2017-09-20 | 2020-07-03 | 吉林大学 | ARM processor-based corn lncRNA screening and classifying method |
| 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 |
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