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Search Results: 1 - 9 of 9 matches for " pseudoknot "
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Approximation Algorithm and Scheme for RNA Maximum Weighted Stacking
Hengwu Li,Huijian Han,Zhenzhong Xu
Journal of Software , 2011, DOI: 10.4304/jsw.6.2.233-240
Abstract: Pseudoknotted RNA structure prediction is an important problem in bioinformatics. Existing polynomial time algorithms have no performance guarantee or can handle only limited types of pseudoknots. In this paper for the general problem of pseudoknotted RNA structure prediction, maximum weighted stacking problem is presented based on stacking actions, and its polynomial time approximation algorithm with O(nlogn) time and O(n) space and polynomial time approximation scheme are given. The approximate performance ratio of this approximation algorithm is 3. Compared with existing polynomial time algorithm, they have exact approximation performance and can predict arbitrary pseudoknots.
Prediction for RNA planar pseudoknots
Li Hengwu,Zhu Daming,Liu Zhendong,Li Hong,
Li Hengwu
,Zhu Daming,Liu Zhendong and Li Hong

自然科学进展 , 2007,
Abstract: Based on m-stems and semi-extensible structure, a model is presented to represent RNA planar pseudoknots, and corresponding dynamic programming algorithm is designed and implemented to predict arbitrary planar pseudoknots and simple non-planar pseudoknots with O(n4) time and O(n3) space. The algorithm folds total 245 sequences in the Pseudobase database, and the test results indicate that the algorithm has good accuracy, sensitivity and specificity.
Altering SARS Coronavirus Frameshift Efficiency Affects Genomic and Subgenomic RNA Production
Ewan P. Plant,Amy C. Sims,Ralph S. Baric,Jonathan D. Dinman,Deborah R. Taylor
Viruses , 2013, DOI: 10.3390/v5010279
Abstract: In previous studies, differences in the amount of genomic and subgenomic RNA produced by coronaviruses with mutations in the programmed ribosomal frameshift signal of ORF1a/b were observed. It was not clear if these differences were due to changes in genomic sequence, the protein sequence or the frequency of frameshifting. Here, viruses with synonymous codon changes are shown to produce different ratios of genomic and subgenomic RNA. These findings demonstrate that the protein sequence is not the primary cause of altered genomic and subgenomic RNA production. The synonymous codon changes affect both the structure of the frameshift signal and frameshifting efficiency. Small differences in frameshifting efficiency result in dramatic differences in genomic RNA production and TCID50 suggesting that the frameshifting frequency must stay above a certain threshold for optimal virus production. The data suggest that either the RNA sequence or the ratio of viral proteins resulting from different levels of frameshifting affects viral replication.
PSEUDOKNOTS IN HUMAN SNRNPS
SANJAY KUMAR DEY, SAYAK GANGULI, PAUSHALI ROY, PROTIP BASU, HIRAK JYOTI CHAKRABORTY AND ABHIJIT DATTA
International Journal of Bioinformatics Research , 2011,
Abstract: Snurps or small nuclear ribonucleoproteins (snRNPs), are RNA-protein complexes that combine withunmodified pre-mRNA and various other proteins to form a Spliceosome, comprising of five small nuclear RNAs(snRNAs)—U1, U2, U4, U5, and U6 snRNA—as well as many protein factors, upon which splicing of pre-mRNAoccurs. While, RNA pseudoknots play crucial role in protein synthesis by helping in internal ribosome entry,frameshifting, stop codon readthrough in many viral species and the 3’NCR pseudoknots helps viral RNAs to replicate,has been reported by a number of investigators, its presence in human snurps has not yet been done. The present insilico study reveals the presence of pseudoknots in the mRNAs of the proteins associated with human Spliceosome. Itnot only emphasizes their significance as catalytic RNA world relics but also opens the scope of research in thefunctional and structural associations of RNA pseudoknots in eukaryotic gene regulation.
Multi-Objective Genetic Algorithm for Pseudoknotted RNA Sequence Design
Akito Taneda
Frontiers in Genetics , 2012, DOI: 10.3389/fgene.2012.00036
Abstract: RNA inverse folding is a computational technology for designing RNA sequences which fold into a user-specified secondary structure. Although pseudoknots are functionally important motifs in RNA structures, less reports concerning the inverse folding of pseudoknotted RNAs have been done compared to those for pseudoknot-free RNA design. In this paper, we present a new version of our multi-objective genetic algorithm (MOGA), MODENA, which we have previously proposed for pseudoknot-free RNA inverse folding. In the new version of MODENA, (i) a new crossover operator is implemented and (ii) pseudoknot prediction methods, IPknot and HotKnots, are used to evaluate the designed RNA sequences, allowing us to perform the inverse folding of pseudoknotted RNAs. The new version of MODENA with the new crossover operator was benchmarked with a dataset composed of natural pseudoknotted RNA secondary structures, and we found that MODENA can successfully design more pseudoknotted RNAs compared to the other pseudoknot design algorithm. In addition, a sequence constraint function newly implemented in the new version of MODENA was tested by designing RNA sequences which fold into the pseudoknotted structure of a hepatitis delta virus ribozyme; as a result, we successfully designed eight RNA sequences. The new version of MODENA is downloadable from http://rna.eit.hirosaki-u.ac.jp/modena/.
An RNA Secondary Structure Prediction Algorithm Based on Fast Dynamic Weighted Matching
基于快速动态权重匹配的RNA二级结构预测算法

骆嘉伟,彭政
计算机应用 , 2008,
Abstract: 在动态权重匹配算法的基础上提出了基于快速动态权重匹配的RNA二级结构预测算法.通过引入最大动态权重茎区搜索算法降低时间复杂度和扩大搜索假结的区域提高预测假结的能力,使得快速动态权重匹配算法与动态权重匹配算法相比,不仅具有O(n3)的更加理想的时间复杂度,而且还能预测更多可能存在的假结.
Two Pseudoknots from Human C2H2 Zinc Finger Genes Discovered by Computational Structure Analysis
Shaowu Meng,Zhuo Zhang
Biotechnology , 2005,
Abstract: Pseudoknots have been extensively identified in viruses. However, very few pseudoknots in Human genome have been previously reported. In this study, we identify two pseudoknots in mRNAs of two separate C2H2 zinc finger (C2H2-ZNF) genes after studying the entire 226 C2H2-ZNF genes in Human Chromosome 19 through using standard tools in an original manner, such as searching Pfam database and analyzing the primary structure of these genes and the secondary structure of their putative mRNAs. The two pseudoknots are different in structure and one of them is very likely to stimulate +1 programmed ribosomal frameshifting. We also found some interesting characteristics of the two genes: each gene has significant C2H2-ZNF domains (e-2 or better) in two ORFs of different reading frames; the two ORFs each have a promoter, a transcription start site, a start codon, a Kozak pattern, a Poly(A) site and a Poly(A) signal and thus each of them can be viewed as a gene. Moreover, we compare these two pseudoknots with the structures of the reported pseudoknots in mammals. Present discovery would be useful in the deeper understanding of structural characteristics and functions of pseudoknots.
RNA Structural Homology Search with a Succinct Stochastic Grammar Model
Ying-Lei Song,Ji-Zhen Zhao,Chun-Mei Liu,Kan Liu,Russell Malmberg,Li-Ming Cai,
Ying-Lei Song
,Ji-Zhen Zhao,Chun-MeiLiu,Kan Liu,Russell Malmberg,and Li-MingCai

计算机科学技术学报 , 2005,
Abstract: An increasing number of structural homology search tools, mostly based on profile stochastic context-free grammars (SCFGs) have been recently developed for the non-coding RNA gene identification. SCFGs can include statistical biases that often occur in RNA sequences, necessary to profile specific RNA structures for structural homology search. In this paper, a succinct stochastic grammar model is introduced for RNA that has competitive search effectiveness. More importantly, the profiling model can be easily extended to include pseudoknots, structures that are beyond the capability of profile SCFGs. In addition, the model allows heuristics to be exploited, resulting in a significant speed-up for the CYK algorithm-based search.
A +1 Programmed Ribosomal Frameshifting of a Human C2H2 Zinc Finger Gene Discovered by Computational Analysis
Shaowu Meng,Zhuo Zhang,Limsoon Wong
Biotechnology , 2005,
Abstract: In this study, we discover a +1 programmed ribosomal frameshifting in a human C2H2 zinc finger (C2H2-ZNF) gene after testing total 226 C2H2-ZNF genes in Human Chromosome 19 through using an original combination of standard computational tools. Our evidences are as follows: Firstly, this zinc finger gene, denoted Z3-7, has significant C2H2-ZNF domains (e-value<0.05) in its two ORFs in different reading frames. Secondly, the two ORFs are overlapped, with a common promoter, a common transcription start site, but with different start codons, different Kozak patterns, different PolyA sites and different PolyA signals. Thirdly, in the mRNA of this gene, we found a significant pseudoknot and a likely frameshifting sites UUUCCU, five upstream nucleotides before this pseudoknot; Moreover, each of the two ORFs of Z3-7 significantly matches two reading frames of seven human C2H2-ZNF ESTs (e-value<10 20 ) and of three human C2H2-ZNF cDNAs (e-value<10 30) that correspond to human C2H2-ZNF proteins. More importantly, each of the two ORFs of Z3-7 significantly matches human C2H2-ZNF proteins (e-value<10 30). These facts indicate that each of the two ORFs of Z3-7 could be transcribed and translated in vivo and that the ribosomal frameshifting of Z3-7 is likely efficient. The present discovery would be helpful for deeper understanding of the regulatory mechanism of a gene with tandem repetitive domains and should have potential to understand and cure diseases caused by abnormality in such transcription factors as C2H2-ZNF proteins.
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