From consensus structure prediction to RNA gene finding (Q28261562)

Briefings in functional genomics & proteomics

Europe PubMed Central

title

From consensus structure prediction to RNA gene finding (English)

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Ivo L Hofacker

2

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author name string

Stephan H Bernhart

series ordinal

1

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language of work or name

English

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publication date

November 2009

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published in

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Toward the 1,000 dollars human genome.

PubMed

volume

8

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issue

6

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page(s)

461-71

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cites work

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Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information

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Fast algorithm for predicting the secondary structure of single-stranded RNA

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Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction

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A comprehensive comparison of comparative RNA structure prediction approaches

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Secondary structure prediction for aligned RNA sequences

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Measuring covariation in RNA alignments: physical realism improves information measures

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RSEARCH: finding homologs of single structured RNA sequences

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XRate: a fast prototyping, training and annotation tool for phylo-grammars

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Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction

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CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

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An enhanced RNA alignment benchmark for sequence alignment programs

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Pfold: RNA secondary structure prediction using stochastic context-free grammars

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Evolutionary trees from DNA sequences: A maximum likelihood approach

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The equilibrium partition function and base pair binding probabilities for RNA secondary structure

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RNAalifold: improved consensus structure prediction for RNA alignments

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An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots

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RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers

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BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences

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Complete suboptimal folding of RNA and the stability of secondary structures

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Robust prediction of consensus secondary structures using averaged base pairing probability matrices

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Automatic detection of conserved RNA structure elements in complete RNA virus genomes

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ConStruct: a tool for thermodynamic controlled prediction of conserved secondary structure

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ConStruct: Improved construction of RNA consensus structures

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Finding the most significant common sequence and structure motifs in a set of RNA sequences

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Dynalign: an algorithm for finding the secondary structure common to two RNA sequences

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Accelerated probabilistic inference of RNA structure evolution

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Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

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Alignment of RNA base pairing probability matrices

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Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

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Multiple structural alignment and clustering of RNA sequences

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Prediction of common secondary structures of RNAs: a genetic algorithm approach

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Finding the common structure shared by two homologous RNAs.

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

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1 reference

MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing

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1 reference

SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework

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CMfinder--a covariance model based RNA motif finding algorithm

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RNA sequence analysis using covariance models

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WAR: Webserver for aligning structural RNAs

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Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs

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Strategies for measuring evolutionary conservation of RNA secondary structures

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Noncoding RNA gene detection using comparative sequence analysis

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Identification and classification of conserved RNA secondary structures in the human genome

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Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures

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A comparative method for finding and folding RNA secondary structures within protein-coding regions

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Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics

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Fast and reliable prediction of noncoding RNAs

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The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures

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Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome

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Genome-wide discovery and verification of novel structured RNAs in Plasmodium falciparum

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Dinucleotide controlled null models for comparative RNA gene prediction

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Tools for simulating evolution of aligned genomic regions with integrated parameter estimation

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Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure

21 January 2018

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Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change

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Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

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Structured RNAs in the ENCODE selected regions of the human genome

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release_w6oxxm76svhhzauzgulabco2xa

21 January 2018

Identifiers

DOI

10.1093/BFGP/ELP043

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Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/w6oxxm76svhhzauzgulabco2xa