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Predictions of RNA secondary structure by combining homologous sequence information

Michiaki Hamada, Kengo Sato, Hisanori Kiryu, Toutai Mituyama, Kiyoshi Asai
2009 Computer applications in the biosciences : CABIOS  
Results: In this article, we propose a new method for secondary structure predictions of individual RNA sequences by taking the information of their homologous sequences into account without assuming the  ...  for predicting the common secondary structure of the homologous sequences.  ...  (M1) Predict a secondary structure of a target RNA sequence x without using homologous sequence information.  ... 
doi:10.1093/bioinformatics/btp228 pmid:19478007 pmcid:PMC2687982 fatcat:bx56bl5gtrd5zodipfxeg6yubi

Predicting RNA secondary structure by the comparative approach: how to select the homologous sequences

Stéfan Engelen, Fariza Tahi
2007 BMC Bioinformatics  
Conclusion: SSCA is an algorithm for selecting combinations of RNA homologous sequences suitable for secondary structure predictions with the comparative approach.  ...  While many possible combinations of homologous sequences may be used for prediction, only a few will give good structure predictions.  ...  The secondary structure of an RNA can be predicted from thermodynamic studies or by comparative studies.  ... 
doi:10.1186/1471-2105-8-464 pmid:18045491 pmcid:PMC2238770 fatcat:rnwzeidsdfhhhfbiutjuntrogq

Study of RNA Secondary Structure Prediction Algorithms

Ying Sun, Sheng Hua Ye, Hong Wei Lu
2011 Advanced Materials Research  
The main development directions of RNA secondary structure prediction algorithm is also be indicated.  ...  RNA secondary structure study is one of the most important fields in computational molecular biology. According to different conditions, RNA secondary structure prediction derives two ways.  ...  They want to determine the consistent structure of this group of homologous sequences by comparing and analyzing multiple homologous sequences, and then determine the secondary structure of RNA.  ... 
doi:10.4028/ fatcat:4ocijgjyhndj7oud6m374ir4ni

rboAnalyzer: A Software to Improve Characterization of Non-coding RNAs From Sequence Database Search Output

Marek Schwarz, Jiří Vohradský, Martin Modrák, Josef Pánek
2020 Frontiers in Genetics  
represented by full-length subject sequences to the query RNA, (3) pooling information across homologous RNAs found in the search results and public databases such as Rfam to predict more reliable secondary  ...  Using predicted full-length matches improves secondary structure prediction and makes rboAnalyzer robust with regards to identification of homology.  ...  fq-sub (2) Secondary structure of query sequence predicted by RNAfold is used to select the best of suboptimal secondary structures generated by hybrid-ss-min prediction + Useful when secondary structure  ... 
doi:10.3389/fgene.2020.00675 pmid:32849767 pmcid:PMC7401326 fatcat:fqkc5vxp5fh63griil4xrd7eje

Computational RNA Structure Prediction

Marc Marti-Renom, Emidio Capriotti
2008 Current Bioinformatics  
In this review, we outline the general principles that govern RNA structure and describe the databases and algorithms for analyzing and predicting RNA secondary and tertiary structure.  ...  Despite advances in understanding the folding and unfolding of RNA, our knowledge of the atomic mechanism by which RNA molecules adopt their biological active structure is still limited.  ...  However, the detection of RNA homology for molecules with diverse sequence is not trivial and additional information such a predicted secondary structure may ensure a higher accuracy in both sequence homology  ... 
doi:10.2174/157489308783329823 fatcat:rpo3hjt2nzgkzdgkhumwz7kmou

A Review on Recent Computational Methods for Predicting Noncoding RNAs

Yi Zhang, Haiyun Huang, Dahan Zhang, Jing Qiu, Jiasheng Yang, Kejing Wang, Lijuan Zhu, Jingjing Fan, Jialiang Yang
2017 BioMed Research International  
structures) are suggested to be combined with the next- and third-generation sequencing platforms to improve ncRNA prediction.  ...  involving evolutionarily conserved RNA sequences and structures, (2) de novo methods using RNA sequence and structure features, (3) transcriptional sequencing and assembling based methods, that is, methods  ...  Conflicts of Interest The authors declare that they have no conflicts of interest. Authors' Contributions  ... 
doi:10.1155/2017/9139504 pmid:28553651 pmcid:PMC5434267 fatcat:gwcnzcftrfgmpiaeepmqfrbogq

TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs

Zhen Tan, Yinghan Fu, Gaurav Sharma, David H. Mathews
2017 Nucleic Acids Research  
This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs.  ...  Probabilities for alignment of nucleotide positions between all pairs of input sequences are iteratively estimated in TurboFold II by incorporating information from both the sequence identity and secondary  ...  This paper describes TurboFold II, which is an extension of the original TurboFold algorithm (38) . TurboFold predicts secondary structures for a set of homologous RNA sequences.  ... 
doi:10.1093/nar/gkx815 pmid:29036420 pmcid:PMC5714223 fatcat:j3sy2g73izaelefbtzvlav5eba

Novel representation of RNA secondary structure used to improve prediction algorithms

Q. Zou, C. Lin, X.-Y. Liu, Y.-P. Han, W.-B. Li, M.-Z. Guo
2011 Genetics and Molecular Research  
When dealing with a single-RNA sequence, the minimum free-energy model is improved by combining it with RNA class information.  ...  We propose a novel representation of RNA secondary structure for a quick comparison of different structures.  ...  ACKNOWLEDGMENTS Research supported by the Natural Science Foundation of China (under grant #61001013, #60932008 and #61172098).  ... 
doi:10.4238/vol10-3gmr1181 pmid:21948761 fatcat:fzy7xe3gpvd77pps32sariuvdi

Computational Approaches in Detecting Non- Coding RNA

Chunyu Wang, Leyi Wei, Maozu Guo, Quan Zou
2013 Current Genomics  
This paper aims to introduce major computational approaches in the identification of ncRNAs, including homologous search, de novo prediction and mining in deep sequencing data.  ...  The important role of non coding RNAs (ncRNAs) in the cell has made their identification a critical issue in the biological research.  ...  ACKNOWLEDGEMENTS The work was supported by the Natural Science  ... 
doi:10.2174/13892029113149990005 pmid:24396270 pmcid:PMC3861888 fatcat:43icugsl6bd4rc7iglozlmsyje

Tfold: efficient in silico prediction of non-coding RNA secondary structures

Stéfan Engelen, Fariza Tahi
2010 Nucleic Acids Research  
Tfold takes as input a RNA sequence for which the secondary structure is searched and a set of aligned homologous sequences.  ...  In this article, we propose an algorithm called Tfold, for predicting non-coding RNA secondary structures.  ...  Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkp1067 pmid:20047957 pmcid:PMC2853104 fatcat:7xyca2pr7rc35lydcxxin2k6ke

RNAcmap: A Fully Automatic Method for Predicting Contact Maps of RNAs by Evolutionary Coupling Analysis [article]

Tongchuan Zhang, Jaswinder Singh, Thomas Litfin, Jian Zhan, Kuldip Paliwal, Yaoqi Zhou
2020 bioRxiv   pre-print
Reliable base-pairing information generated from RNAcmap, for RNAs with high effective homologous sequences, in particular, will be useful for aiding RNA structure prediction.  ...  Motivation: The accuracy of RNA secondary and tertiary structure prediction can be significantly improved by using structural restraints derived from evolutionary or direct coupling analysis.  ...  Using a predicted secondary structure in the RNAcmap greatly expanded the coverage of homologous sequences, resulting in a much more accurate prediction.  ... 
doi:10.1101/2020.08.08.242636 fatcat:r5q2tpgiufdrpnwhrnbb44mg6a

Direct Information Reweighted by Contact Templates: Improved RNA Contact Prediction by Combining Structural Features [article]

Yiren Jian, Chen Zeng, Yunjie Zhao
2017 arXiv   pre-print
These results suggest that DIRECT could be used for improving predictions of RNA tertiary structures and functions.  ...  DCA and similar approaches that use sequence information alone usually yield a low accuracy, especially when the available homologous sequences are limited.  ...  Acknowledgments Author Contributions YR performs most computational analysis under the supervision of CZ and YZ. YZ and CZ supervise the overall study and write the paper.  ... 
arXiv:1711.10674v1 fatcat:c7d676ihjfbhrezqwqlwpbnvqi

CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences

Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C. Frith, Kiyoshi Asai
2011 Nucleic Acids Research  
Although secondary structure predictions of an individual RNA sequence have been widely used in a number of sequence analyses of RNAs, accuracy is still limited.  ...  Recently, we proposed a method (called 'CentroidHomfold'), which includes information about homologous sequences into the prediction of the secondary structure of the target sequence, and showed that it  ...  Then, it estimates a secondary structure of the target sequence using the information in the homologous sequences.  ... 
doi:10.1093/nar/gkr290 pmid:21565800 pmcid:PMC3125741 fatcat:ren5lnxmjraddl4xypmxcldgce

TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

Arif O Harmanci, Gaurav Sharma, David H Mathews
2011 BMC Bioinformatics  
Conclusions: TurboFold is an iterative probabilistic method for predicting secondary structures for multiple RNA sequences that efficiently and accurately combines the information from the comparative  ...  The prediction of secondary structure, i.e. the set of canonical base pairs between nucleotides, is a first step in developing an understanding of the function of an RNA sequence.  ...  Authors were funded by the University of Rochester and by the National Institutes of Health to pay the open access publication charges for this article.  ... 
doi:10.1186/1471-2105-12-108 pmid:21507242 pmcid:PMC3120699 fatcat:5jhxp3tndrcc5piwsyyxwle45u

ILM: a web server for predicting RNA secondary structures with pseudoknots

J. Ruan, G. D. Stormo, W. Zhang
2004 Nucleic Acids Research  
The ILM web server provides a web interface to two algorithms, iterated loop matching, and maximum weighted matching, for the analysis of RNA secondary structures with pseudoknots.  ...  The algorithms can utilize either thermodynamic or comparative information or both, thus is able to predict for both aligned and individual sequences.  ...  Acknowledgements This research was supported in part by NSF grants IIS-0196057 and ITR/EIA-011361 8. GDS was supported by NIH grant HG00249.  ... 
doi:10.1093/nar/gkh444 pmid:15215368 pmcid:PMC441582 fatcat:45zhe2epenfblk426j22titxbm
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