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Approximation Algorithms for Optimal RNA Secondary Structures Common to Multiple Sequences

T. TAMURA, T. AKUTSU
2007 IEICE Transactions on Fundamentals of Electronics Communications and Computer Sciences  
We also show that the problem to optimize structure and alignments for given N sequences is NP-hard and introduce a constant-factor approximation algorithm.  ...  In this paper, we show an O(n 5 ) time approximation algorithm for optimizing structure and alignments of two RNA sequences with assuming that the optimal number of base-pairs is more than O(n 0.75 ).  ...  In RNA0(N ), such a structure is also called an optimal N-common RNA secondary structure, and denoted by OP T (RNA 0 (N )). 3 1 − approximation algorithm for RNA 0 (2) As mentioned above, in RNA 0 (2),  ... 
doi:10.1093/ietfec/e90-a.5.917 fatcat:fssmkwwnlfd3rbu3em26ausef4

A Web Server for Multi-objective Pairwise RNA Sequence Alignment with an Index for Selecting Accurate Alignments

Akito Taneda
2011 IPSJ Transactions on Bioinformatics  
Recently, we have proposed a multi-objective genetic algorithm, Co-folga2mo, for obtaining an approximate set of weak Pareto optimal solutions for global pairwise RNA sequence alignment, where a sequence  ...  similarity and a secondary structure contribution are taken into account as objective functions.  ...  Acknowledgments We would like to thank the anonymous reviewers for their kind comments. This work was supported by KAKENHI (22700304).  ... 
doi:10.2197/ipsjtbio.4.2 fatcat:al2w4aj5n5bivkvwqh4cvaxole

A Classification of Bioinformatics Algorithms from the Viewpoint of Maximizing Expected Accuracy (MEA)

Michiaki Hamada, Kiyoshi Asai
2012 Journal of Computational Biology  
We believe that this review will be useful not only for users wishing to utilize software to solve the estimation problems appearing in this article, but also for developers wishing to design algorithms  ...  In general, it is difficult to design reliable estimators for this type of problem, because the number of possible solutions is immense, which leads to an extremely low probability for every solution-even  ...  ACKNOWLEDGMENTS We are grateful to Dr. Martin C. Frith for commenting on the manuscript. This work was supported in part by a Grant-in-Aid for Scientific Research on Innovative Areas in Japan.  ... 
doi:10.1089/cmb.2011.0197 pmid:22313125 pmcid:PMC3342518 fatcat:pxcpeagqqjb5vbfj532nsbgxpu

CentroidAlign-Web: A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs

Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
2013 International Journal of Molecular Sciences  
Due to the recent discovery of non-coding RNAs (ncRNAs), multiple sequence alignment (MSA) of those long RNA sequences is becoming increasingly important for classifying and determining the functional  ...  However, not only primary (nucleotide) sequences, but also secondary structures of ncRNAs are closely related to their function and are conserved evolutionarily.  ...  Acknowledgments This work was supported in part by MEXT KAKENHI (Grant-in-Aid for Young Scientists (A):  ... 
doi:10.3390/ijms14036144 pmid:23507751 pmcid:PMC3634467 fatcat:me7y2czkija7hl4ctfqdnaaztq

RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment

X. Xu, Y. Ji, G. D. Stormo
2007 Bioinformatics  
Methods and Results: We present a new sampling based algorithm to predict common RNA secondary structures in multiple unaligned sequences.  ...  Predicting common RNA secondary structures in multiple unaligned sequences remains a challenge in bioinformatics research.  ...  We thank the authors of all software used or tested in this study for making their software publicly available.  ... 
doi:10.1093/bioinformatics/btm272 pmid:17537756 fatcat:k62drh7nzfgofbttlflwdaw3lq

Multiple Structural RNA Alignment with Lagrangian Relaxation [chapter]

Markus Bauer, Gunnar W. Klau, Knut Reinert
2005 Lecture Notes in Computer Science  
We present a formulation for computing provably optimal, structurebased, multiple RNA alignments and give an algorithm that finds such an optimal solution or at least a very good approximation of it.  ...  In contrast to proteins, many classes of functionally related RNA molecules show a rather weak sequence conservation but instead a fairly well conserved secondary structure.  ...  The authors thank Ernst Althaus for help with incorporating the code for exact multiple sequence alignments into the prototype of mLARA and thank Ivo Hofacker for helpful discussions.  ... 
doi:10.1007/11557067_25 fatcat:5gk6lwf3g5cgrhowbdel3lgim4

CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score

M. Hamada, K. Sato, H. Kiryu, T. Mituyama, K. Asai
2009 Bioinformatics  
Motivation: The importance of accurate and fast predictions of multiple alignments for RNA sequences has increased due to recent findings about functional non-coding RNAs.  ...  Results: We designed a novel estimator for multiple alignments of structured RNAs, based on maximizing the expected accuracy of predictions.  ...  Lawrence for valuable comments. The authors are also grateful to our colleagues at the Computational Biology Research Center (CBRC) for fruitful discussions.  ... 
doi:10.1093/bioinformatics/btp580 pmid:19808876 fatcat:jdnrvt5x7jfqpmg3khc2tj6bk4

Iterative estimation of structures of multiple RNA homologs: Turbofold

Gaurav Sharma, A. Ozgun Harmanci, David H. Mathews
2011 2011 IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP)  
TurboFold, an iterative algorithm for estimating the common secondary structures of multiple RNA homologs, is presented.  ...  Instead of solving the joint problem of aligning and folding multiple RNA sequences, TurboFold uses an iterative process to fold a collection of RNA homologs.  ...  sequence, these tools are extended and applied to multiple RNA homologs, i.e. evolutionarily related RNA sequences that serve the same function and therefore share common 1 secondary structure.  ... 
doi:10.1109/icassp.2011.5946457 dblp:conf/icassp/SharmaHM11 fatcat:ims57ncxzvfqxbbqanvzowuoee

Multi-objective pairwise RNA sequence alignment

Akito Taneda
2010 Computer applications in the biosciences : CABIOS  
RNA sequence alignment problem has been investigated by many researchers as a mono-objective optimization problem where contributions from sequence similarity and secondary structure are taken into account  ...  So far, no one has examined how good alignments we can obtain by applying multi-objective optimization to structural RNA sequence alignment problem.  ...  To emphasize on the inclusion of secondary structure score, we refer to RNA sequence alignment as 'structural RNA sequence alignment' in the present article.  ... 
doi:10.1093/bioinformatics/btq439 pmid:20679330 fatcat:kyubjg6hz5g2ppuzdhrqdv4bim

RNA sequence analysis using covariance models

Sean R. Eddy, Richard Durbin
1994 Nucleic Acids Research  
We describe a general approach to several RNA sequence analysis problems using probabilistic models that flexibly describe the secondary structure and primary sequence consensus of an RNA sequence family  ...  We also describe an algorithm for learning a model and hence a consensus secondary structure from initially unaligned example sequences and no prior structural information.  ...  , for some of our computer time.  ... 
doi:10.1093/nar/22.11.2079 pmid:8029015 pmcid:PMC308124 fatcat:brjelnyxgjhe7frobebagr4l3m

RNA Secondary Structure Prediction from Multi-Aligned Sequences [chapter]

Michiaki Hamada
2014 Msphere  
In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted.  ...  ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome.  ...  (b) Common (or consensus) RNA secondary structure prediction in which the input is a multiple sequence alignment of RNA sequences and the output is an RNA secondary structure whose length is equal to the  ... 
doi:10.1007/978-1-4939-2291-8_2 pmid:25577370 fatcat:5txbrogzq5eu7gi2yjk22fewv4

RNA secondary structure prediction from multi-aligned sequences [article]

Michiaki Hamada
2013 arXiv   pre-print
In this review, I focus on common secondary structure prediction from a given aligned RNA sequence, in which one secondary structure whose length is equal to that of the input alignment is predicted.  ...  ncRNAs but also to improve the accuracy of secondary structure predictions and to find novel functional RNAs from the genome.  ...  (b) Common (or consensus) RNA secondary structure prediction in which the input is a multiple sequence alignment of RNA sequences and the output is an RNA secondary structure whose length is equal to the  ... 
arXiv:1307.1934v1 fatcat:qma53lxhdje5fjjinnscamiitq

Pure multiple RNA secondary structure alignments: a progressive profile approach

M. Hochsmann, B. Voss, R. Giegerich
2004 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
We provide a purely structure-based approach for comparing multiple RNA secondary structures.  ...  We provide a method for computing multiple alignments of RNA secondary structures under the tree alignment model, which is suitable to cluster RNA molecules purely on the structural level, i.e., sequence  ...  EXPERIMENTS Multiple alignment of RNA secondary structures is helpful to reveal a common structural property of RNAs.  ... 
doi:10.1109/tcbb.2004.11 pmid:17048408 fatcat:kvjnbbkhmre7nltdfoqi77pcgy

Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures

Yutaka Saito, Kengo Sato, Yasubumi Sakakibara
2011 BMC Bioinformatics  
Instead, our method utilizes all possible sequence alignments and all possible secondary structures, whereas the existing methods only use one optimal sequence alignment and one optimal secondary structure  ...  However, the high computational cost of exact structural alignment requires these methods to employ approximate algorithms.  ...  The idea of our similarity measure is to approximate the Sankoff algorithm for structural alignment by the combination of the SW algorithm for sequence alignment, and the McCaskill algorithm for secondary  ... 
doi:10.1186/1471-2105-12-s1-s48 pmid:21342580 pmcid:PMC3044305 fatcat:siyuq6tczne2zbwonbyrtd7kla

A Perspective on the Algorithms Predicting and Evaluating the RNA Secondary Structure

Giulia Fiscon
2016 Journal of Genetics and Genome Research  
Indeed, functional RNAs show specific instrumental sub-structures for their interaction with other molecules.  ...  Investigating the RNA structure contributes greatly to understand RNA roles in cellular processes.  ...  Comparative approaches These methods predict the RNA secondary structure starting from multiple sequences in order to find the more conservative one (consensus structure) common to all (or almost all)  ... 
doi:10.23937/2378-3648/1410023 fatcat:acdxcj7pmbfjnmzu3prw732wve
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