About: An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots

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About: An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots
Creator	Juanjuan, He Jun, Liu Kai, Zhang Yulin, Lv Yuting, Wang
Source	PMC
abstract	BACKGROUND: RNA pseudoknot structures play an important role in biological processes. However, existing RNA secondary structure prediction algorithms cannot predict the pseudoknot structure efficiently. Although random matching can improve the number of base pairs, these non-consecutive base pairs cannot make contributions to reduce the free energy. RESULT: In order to improve the efficiency of searching procedure, our algorithm take consecutive base pairs as the basic components. Firstly, our algorithm calculates and archive all the consecutive base pairs in triplet data structure, if the number of consecutive base pairs is greater than given minimum stem length. Secondly, the annealing schedule is adapted to select the optimal solution that has minimum free energy. Finally, the proposed algorithm is evaluated with the real instances in PseudoBase. CONCLUSION: The experimental results have been demonstrated to provide a competitive and oftentimes better performance when compared against some chosen state-of-the-art RNA structure prediction algorithms.
has issue date	2019-12-27(xsd:dateTime)
bibo:doi	10.1186/s12864-019-6300-2
bibo:pmid	31881969
has license	cc-by
sha1sum (hex)	f73808579d362b40e0f9c8ef0d87868a0e3e3481
schema:url	https://doi.org/10.1186/s12864-019-6300-2
resource representing a document's title	An efficient simulated annealing algorithm for the RNA secondary structure prediction with Pseudoknots
has PubMed Central identifier	PMC6933665
has PubMed identifier	31881969
schema:publication	BMC Genomics
resource representing a document's body	covid:f73808579d362b40e0f9c8ef0d87868a0e3e3481#body_text
is schema:about of	named entity 'ALGORITHM' named entity 'RNA' named entity 'number' named entity 'base pairs' named entity 'algorithm' named entity 'schedule' named entity 'simulated annealing' named entity 'EFFICIENT' named entity 'SIMULATED ANNEALING' named entity 'RNA' named entity 'BASIC' named entity 'FREE ENERGY' named entity 'SCHEDULE' named entity 'PLAY' named entity 'BIOLOGICAL PROCESSES' named entity 'PREDICT' named entity 'ARCHIVE' named entity 'STRUCTURES' named entity 'ANNEALING' named entity 'STRUCTURE' named entity 'STEM LENGTH' named entity 'PSEUDOKNOT' named entity 'GIVEN' named entity 'SOLUTION' named entity 'NUMBER OF' named entity 'SELECT' named entity 'EVALUATED' named entity 'OPTIMAL' named entity 'RANDOM' named entity 'MATCHING' named entity 'BASE PAIRS' named entity 'MINIMUM' named entity 'ADAPTED' named entity 'ALGORITHM' named entity 'PREDICTION ALGORITHMS' named entity 'BACKGROUND' named entity 'TRIPLET' named entity 'THESE' named entity 'ORDER' named entity 'SECONDLY' named entity 'RNA SECONDARY STRUCTURE PREDICTION' named entity 'ROLE' named entity 'IMPORTANT' named entity 'RESULT' named entity 'RNA SECONDARY STRUCTURE PREDICTION' named entity 'NON-' named entity 'CONSECUTIVE' named entity 'DATA STRUCTURE' named entity 'MAKE' named entity 'TO REDUCE' named entity 'PSEUDOKNOTS' named entity 'OUR' named entity 'REAL' named entity 'PROCEDURE' named entity 'EFFICIENCY' named entity 'PROPOSED' named entity 'GREATER THAN' named entity 'FIRSTLY' named entity 'COMPONENTS' covid:arg/f73808579d362b40e0f9c8ef0d87868a0e3e3481 named entity 'reduce' named entity 'random' named entity 'base pairs' named entity 'triplet' named entity 'structures' named entity 'improve' named entity 'base pairs' named entity 'minimum free energy' named entity 'base pairs' named entity 'algorithm' named entity 'RNA structure' named entity 'phosphoric acid' named entity 'Guanine' named entity 'base pairs' named entity 'secondary structure' named entity 'MFE' named entity 'base pairs'

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