TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences (Q24608886)

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

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English	TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences	scientific article	TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences

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scholarly article

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TurboFold: iterative probabilistic estimation of secondary structures for multiple RNA sequences (English)

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object named as

Gaurav Sharma

2

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author name string

Arif O Harmanci

1

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David H Mathews

3

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language of work or name

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publication date

2011

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BMC Bioinformatics

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12

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1

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108

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https://scigraph.springernature.com/pub.10.1186/1471-2105-12-108

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Improving the accuracy of predicting secondary structure for aligned RNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

RNAstructure: software for RNA secondary structure prediction and analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Predictions of RNA secondary structure by combining homologous sequence information

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Accurate SHAPE-directed RNA structure determination

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Differentiating protein-coding and noncoding RNA: challenges and ambiguities

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

RNAalifold: improved consensus structure prediction for RNA alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

PARTS: probabilistic alignment for RNA joinT secondary structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

The tmRDB and SRPDB resources

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

ProbCons: Probabilistic consistency-based multiple sequence alignment

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Fast and reliable prediction of noncoding RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Noncoding RNA gene detection using comparative sequence analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Comparative sequence analysis of tmRNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

The Ribonuclease P Database

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Ribonuclease P: an enzyme with an essential RNA component

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Non–coding RNA genes and the modern RNA world

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

A fast structural multiple alignment method for long RNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Clustal W and Clustal X version 2.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

From consensus structure prediction to RNA gene finding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

CONTRAfold: RNA secondary structure prediction without physics-based models

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Secondary structure of vertebrate telomerase RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

In vitro splicing of the ribosomal RNA precursor of Tetrahymena: involvement of a guanosine nucleotide in the excision of the intervening sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

In vitro splicing of the ribosomal RNA precursor of tetrahymena: Involvement of a guanosine nucleotide in the excision of the intervening sequence

1 reference

https://api.crossref.org/works/10.1186/1471-2105-12-108

22 April 2017

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

Compilation of tRNA sequences and sequences of tRNA genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

7 April 2017

De novo prediction of structured RNAs from genomic sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Improved RNA secondary structure prediction by maximizing expected pair accuracy

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Stochastic sampling of the RNA structural alignment space.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Prediction of RNA secondary structure using generalized centroid estimators

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

A max-margin model for efficient simultaneous alignment and folding of RNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Annotating noncoding RNA genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Multiple structural alignment and clustering of RNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Prediction of RNA secondary structure by free energy minimization

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Revolutions in RNA secondary structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Noncoding RNA transcripts.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

The chemical repertoire of natural ribozymes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

Computational genomics of noncoding RNA genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

5S ribosomal RNA database Y2K

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

RNA structure prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

27 September 2017

The RNA structure alignment ontology

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3120699

30 May 2018

RNAshapes: an integrated RNA analysis package based on abstract shapes.

1 reference

https://api.crossref.org/works/10.1186%2F1471-2105-12-108

21 January 2018

tmRDB (tmRNA database)

1 reference

https://pubmed.ncbi.nlm.nih.gov/21507242

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1186/1471-2105-12-108

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Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

DBLP publication ID

journals/bmcbi/HarmanciSM11

1 reference

DBLP Dataset 2021-01-02

28 January 2021

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OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

ResearchGate publication ID

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