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RNA structure alignment by a unit-vector approach

E. Capriotti, M. A. Marti-Renom
2008 Bioinformatics  
In this article, we introduce a new algorithm for RNA structure alignment based on a unit-vector approach.  ...  A benchmark against the ARTS program using a set of 1275 non-redundant pairwise structure alignments results in ∼6% extra alignments with at least 50% structurally superposed nucleotides and base pairs  ...  ACKNOWLEDGEMENTS We acknowledge support from a Marie Curie International Reintegration Grant (FP6-039722) and Generalitat Valenciana (GV/2007/065).  ... 
doi:10.1093/bioinformatics/btn288 pmid:18689811 fatcat:du7hp2vwcnc63gr3pp7joffwb4

SARA: a server for function annotation of RNA structures

E. Capriotti, M. A. Marti-Renom
2009 Nucleic Acids Research  
The SARA server relies on the SARA program, which aligns two RNA structures based on a unit-vector root-mean-square approach.  ...  Here, we introduce the SARA program for pair-wise alignment of RNA structures as a web server for structure-based RNA function assignment.  ...  to a unit-distance, and place the tails of all normalized vectors at the origin of a unit-sphere; the resulting collection of normalized vectors is the unit-vector representation of the input RNA; (iii  ... 
doi:10.1093/nar/gkp433 pmid:19483098 pmcid:PMC2703911 fatcat:5vtjtyhoajc75hrgumvyrwyr24

A Machine Learning Approach for Accurate Annotation of Noncoding RNAs

Yinglei Song, Chunmei Liu, Zhi Wang
2015 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
In general, the secondary structure of a searched noncoding RNA is defined with a structure model constructed from the structural alignment of a set of sequences from its family.  ...  Computing the optimal alignment between a sequence and a structure model is the core part of an algorithm that can search genomes for noncoding RNAs.  ...  Search Accuracy A software package RNASC (RNA Search by Classification) has been developed to implement our approach.  ... 
doi:10.1109/tcbb.2014.2366758 pmid:26357266 pmcid:PMC4726481 fatcat:iyoubdqc2valpkgabzspjz7ml4

Quantifying the relationship between sequence and three-dimensional structure conservation in RNA

Emidio Capriotti, Marc A Marti-Renom
2010 BMC Bioinformatics  
: (i) there is a measurable relationship between sequence and structure conservation that weakens for alignments resulting in below 60% sequence identity, (ii) evolution tends to conserve more RNA structure  ...  Our work could represent the theoretical basis and limitations for future developments in comparative RNA 3D structure prediction. Table 1: RNA structure and alignments datasets.  ...  Structure-based RNA alignments Pairs of RNA structures were aligned using the SARA program, which is based on the unit vector approach [55] .  ... 
doi:10.1186/1471-2105-11-322 pmid:20550657 pmcid:PMC2904352 fatcat:mjlh42js25d2ndzn4bf3pwys5y

Tracking down noncoding RNAs

V. Moulton
2005 Proceedings of the National Academy of Sciences of the United States of America  
then, by using secondary structure detection approaches, try to decide which of these are alignments of ncRNAs.  ...  However, the preservation of RNA secondary structure in an alignment naturally suggests a comparative genomics approach to finding ncRNAs: form alignments between conserved subsequences of genomes and  ...  then, by using secondary structure detection approaches, try to decide which of these are alignments of ncRNAs.  ... 
doi:10.1073/pnas.0500129102 pmid:15703286 pmcid:PMC549017 fatcat:hmhdljjxxjhyrmf2lalst2lx3i

iPARTS: an improved tool of pairwise alignment of RNA tertiary structures

Chih-Wei Wang, Kun-Tze Chen, Chin Lung Lu
2010 Nucleic Acids Research  
iPARTS is an improved web server for aligning two RNA 3D structures based on a structural alphabet (SA)-based approach.  ...  In particular, we first derive a Ramachandran-like diagram of RNAs by plotting nucleotides on a 2D axis using their two pseudotorsion angles g and h.  ...  Therefore, we believe that iPARTS can serve as a useful tool in the study of structural and functional biology. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online.  ... 
doi:10.1093/nar/gkq483 pmid:20507908 pmcid:PMC2896121 fatcat:42bltn4k5fd7fbvp4nwvy3rdhi

RNAscClust: clustering RNA sequences using structure conservation and graph based motifs

Milad Miladi, Alexander Junge, Fabrizio Costa, Stefan E Seemann, Jakob Hull Havgaard, Jan Gorodkin, Rolf Backofen, Cenk Sahinalp
2017 Bioinformatics  
For a set of multiple structural alignments of RNA sequences, each containing a paralog sequence included in a structural alignment of its orthologs, RNAscClust computes minimum free-energy structures  ...  Whereas structural RNA alignment strategies typically identify common structure for orthologous structured RNAs, clustering seeks to group paralogous RNAs based on structural similarities.  ...  1, BA 2168/4-2, BA 2168/3-3 A to R.B.).  ... 
doi:10.1093/bioinformatics/btx114 pmid:28334186 pmcid:PMC5870858 fatcat:t5yivjrudbgg3o2e7jk5rjbhr4

DNA-Level Splice Junction Prediction using Deep Recurrent Neural Networks [article]

Byunghan Lee, Taehoon Lee, Byunggook Na, Sungroh Yoon
2015 arXiv   pre-print
Experimental techniques for determining exon/intron boundaries include RNA-seq, which is often accompanied by computational approaches.  ...  Precise identification of spice junctions on a gene is important for deciphering its primary structure, function, and interaction.  ...  First, alignment-based methods [5, 6, 7, 8, 9] map short RNA sequences produced by RNA-seq [10] to a reference genome and estimate the splicing sites, identifying the exon locations along with expression  ... 
arXiv:1512.05135v1 fatcat:jjozmraidffntdklr46mazxt2a

Pure multiple RNA secondary structure alignments: a progressive profile approach

M. Hochsmann, B. Voss, R. Giegerich
2004 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
As T-Coffee computes a sequence alignment, this step inherits the problem of pairwise sequence alignments of RNA structures. That is: A base-pair is not treated as a unit.  ...  A tree profile representation of RNA secondary structure alignments makes the progressive approach applicable to multiple RNA structure comparison. As a tree is a fundamental data structure, our  ...  In contrast to the sequence-based approach, structural conserved regions are the anchor regions of the alignment. Clearly, our approach is sensitive to a correct prediction of RNA structures.  ... 
doi:10.1109/tcbb.2004.11 pmid:17048408 fatcat:kvjnbbkhmre7nltdfoqi77pcgy

RNA global alignment in the joint sequence–structure space using elastic shape analysis

Jose Laborde, Daniel Robinson, Anuj Srivastava, Eric Klassen, Jinfeng Zhang
2013 Nucleic Acids Research  
The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. Based on ESA, a rigorous mathematical framework can be built for RNA structure comparison.  ...  The functions of RNAs, like proteins, are determined by their structures, which, in turn, are determined by their sequences.  ...  The difference of nucleotides can be compared via the unit vectors using unit-vector root mean square (URMS) as distance (8, 9) ; iPARTS uses structural alphabet (SA) derived from backbone torsion angles  ... 
doi:10.1093/nar/gkt187 pmid:23585278 pmcid:PMC3675459 fatcat:qgkk6i2pnzaxxhjo77pcudx3zy

Discovering cis-Regulatory RNAs in Shewanella Genomes by Support Vector Machines

Xing Xu, Yongmei Ji, Gary D. Stormo, Hanah Margalit
2009 PLoS Computational Biology  
RSSVM uses a set of distinctive features to represent the common RNA secondary structure and structural alignment predicted by RNA Sampler, a tool for accurate common RNA secondary structure prediction  ...  We present a new computational program named RSSVM (RNA Sampler+Support Vector Machine), which employs Support Vector Machines (SVMs) for efficient identification of functional RNA motifs from random RNA  ...  In such methods, the RNA secondary structures or structural alignments of homologous RNAs are represented by a set of predefined features, and the SVM maps the vectors defined by these features to a high-dimensional  ... 
doi:10.1371/journal.pcbi.1000338 pmid:19343219 pmcid:PMC2659441 fatcat:rctmmfc35ffqph3gqal44kloqm

SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments

Paweł Piątkowski, Jagoda Jabłońska, Adriana Żyła, Dorota Niedziałek, Dorota Matelska, Elżbieta Jankowska, Tomasz Waleń, Wayne K. Dawson, Janusz M. Bujnicki
2017 Nucleic Acids Research  
The accuracy of superpositions was assessed by comparing structure-based sequence alignments to the reference alignments from the Rfam database.  ...  RNA has been found to play an ever-increasing role in a variety of biological processes. The function of most non-coding RNA molecules depends on their structure.  ...  ACKNOWLEDGEMENTS We would like to thank the authors of the benchmarked programs for their help: David Hoksza (SETTER), Emidio Capriotti (SARA), Anton Petrov and Ryan Rahrig (R3D Align), Kristian Rother  ... 
doi:10.1093/nar/gkx631 pmid:28934487 pmcid:PMC5766185 fatcat:3ttdfikyqjamll3lmirjqrw5yi

Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs

Andrew C. Stelzer, Aaron T. Frank, Maximillian H. Bailor, Ioan Andricioaei, Hashim M. Al-Hashimi
2009 Methods  
A broad structural landscape often needs to be characterized in order to fully understand how regulatory RNAs perform their biological functions at the atomic level.  ...  The structural ensembles generated in this manner provide insights into RNA dynamics and its role in functionally important transitions.  ...  One approach to overcome this problem is to elongate a target helix such that the overall RNA shape and hence its overall alignment is dominated by the elongated helix and is no longer as sensitive to  ... 
doi:10.1016/j.ymeth.2009.08.006 pmid:19699798 pmcid:PMC3320149 fatcat:edsscjn63bhstpzxv6zzwsb5fq

Variation in human chromosome 21 ribosomal RNA genes characterized by TAR cloning and long-read sequencing

Jung-Hyun Kim, Alexander T Dilthey, Ramaiah Nagaraja, Hee-Sheung Lee, Sergey Koren, Dawood Dudekula, William H Wood III, Yulan Piao, Aleksey Y Ogurtsov, Koichi Utani, Vladimir N Noskov, Svetlana A Shabalina (+3 others)
2018 Nucleic Acids Research  
TAR cloning and long-read sequencing enabled the accurate reconstruction of multiple rDNA units and a new, high-quality 44 838 bp rDNA reference sequence, which we have annotated with variants detected  ...  from chromosome 21 of a single individual.  ...  Longer BACs included JH11 (vector #6), which contained two tandem rDNA units; JH4 (vector #2), which contained one rDNA unit preceded by a truncated IGS; and JH14 (vector #11), which contained a truncated  ... 
doi:10.1093/nar/gky442 pmid:29788454 pmcid:PMC6061828 fatcat:jxu2gcgrwfcffflt4233tq3xfi

iPARTS2: an improved tool for pairwise alignment of RNA tertiary structures, version 2

Chung-Han Yang, Cheng-Ting Shih, Kun-Tze Chen, Po-Han Lee, Ping-Han Tsai, Jian-Cheng Lin, Ching-Yu Yen, Tiao-Yin Lin, Chin Lung Lu
2016 Nucleic Acids Research  
It was implemented by a structural alphabet (SA)-based approach, which uses an SA of 23 letters to reduce RNA 3D structures into 1D sequences of SA letters and applies traditional sequence alignment to  ...  Since its first release in 2010, iPARTS has become a valuable tool for globally or locally aligning two RNA 3D structures.  ...  As to SETTER, it divides the RNA 3D structure into non-overlapping local structural units, called generalized secondary structure units (GSSUs), and then obtains their structural alignment by using a comparison  ... 
doi:10.1093/nar/gkw412 pmid:27185896 pmcid:PMC4987943 fatcat:o6p2ggxkyncfjm4bmtubsmpvaa
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