ViennaRNA Package 2.0 (Q24053233)

Ronny Lorenz

1

0 references

Hakim Tafer

Hakim Tafer

4

0 references

Christoph Flamm

Christoph Flamm

5

0 references

Ivo L. Hofacker

Ivo L Hofacker

Christian Höner zu Siederdissen

7

0 references

Christian Höner Zu Siederdissen

3

0 references

Stephan H. Bernhart

2

Algorithms for Molecular Biology

Stephan H Bernhart

0 references

publication date

2011

0 references

language of work or name

English

0 references

published in

0 references

volume

6

0 references

issue

1

0 references

page(s)

26

0 references

copyright license

Creative Commons Attribution 2.0 Generic

start time

24 November 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

1 reference

April 2022 Public Data File from Crossref

cites work

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19 March 2017

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RNAalifold: improved consensus structure prediction for RNA alignments

19 March 2017

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Rfam: updates to the RNA families database

19 March 2017

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The Vienna RNA websuite

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

19 March 2017

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MicroTar: predicting microRNA targets from RNA duplexes

19 March 2017

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The Unsuccessful Self-Treatment of a Case of "Writer's Block"

6 April 2017

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Partition function and base pairing probabilities of RNA heterodimers

19 March 2017

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RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble

19 March 2017

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MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence

19 March 2017

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The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search

19 March 2017

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Fast and reliable prediction of noncoding RNAs

19 March 2017

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A comprehensive comparison of comparative RNA structure prediction approaches

19 March 2017

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Fast and effective prediction of microRNA/target duplexes

19 March 2017

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Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction

19 March 2017

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

19 March 2017

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MicroRNA targets in Drosophila

19 March 2017

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A statistical sampling algorithm for RNA secondary structure prediction

19 March 2017

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RSEARCH: finding homologs of single structured RNA sequences

19 March 2017

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

19 March 2017

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A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure

19 March 2017

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Design of multistable RNA molecules

19 March 2017

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

19 March 2017

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

19 March 2017

1 reference

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Improved tools for biological sequence comparison

19 March 2017

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

19 March 2017

1 reference

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Clustal W and Clustal X version 2.0

19 March 2017

1 reference

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

19 March 2017

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The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

19 March 2017

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CONTRAfold: RNA secondary structure prediction without physics-based models

19 March 2017

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The thermodynamics of DNA structural motifs

19 March 2017

1 reference

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Alignment of RNA base pairing probability matrices

19 March 2017

1 reference

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Secondary structure prediction for aligned RNA sequences

19 March 2017

1 reference

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

19 March 2017

1 reference

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Early events in RNA folding

19 March 2017

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

19 March 2017

1 reference

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Accurate and efficient reconstruction of deep phylogenies from structured RNAs

19 March 2017

1 reference

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On finding all suboptimal foldings of an RNA molecule

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Improved Estimation of Secondary Structure in Ribonucleic Acids

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Improved free-energy parameters for predictions of RNA duplex stability

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Rich Parameterization Improves RNA Structure Prediction

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

BioXSD: the common data-exchange format for everyday bioinformatics web services

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Nucleic acid sequence design via efficient ensemble defect optimization

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Improved free energy parameters for RNA pseudoknotted secondary structure prediction

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Prediction of RNA secondary structure using generalized centroid estimators

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

UNAFold: software for nucleic acid folding and hybridization

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNA STRAND: the RNA secondary structure and statistical analysis database

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

SnoReport: computational identification of snoRNAs with unknown targets

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

INFO-RNA--a fast approach to inverse RNA folding.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Memory efficient folding algorithms for circular RNA secondary structures

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Prediction of hybridization and melting for double-stranded nucleic acids

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNAsoft: A suite of RNA secondary structure prediction and design software tools

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNAML: a standard syntax for exchanging RNA information

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNA folding at elementary step resolution

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Estimation of Secondary Structure in Ribonucleic Acids

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Improved predictions of secondary structures for RNA

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

A folding algorithm for extended RNA secondary structures

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNAz 2.0: improved noncoding RNA detection.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Lightweight comparison of RNAs based on exact sequence-structure matches

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNAstrand: reading direction of structured RNAs in multiple sequence alignments

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

taveRNA: a web suite for RNA algorithms and applications

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Complete suboptimal folding of RNA and the stability of secondary structures

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

A computer model of evolutionary optimization

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Fast accessibility-based prediction of RNA-RNA interactions

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

NUPACK: Analysis and design of nucleic acid systems

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNAsnoop: efficient target prediction for H/ACA snoRNAs

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNA secondary structure analysis using the RNAshapes package

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Structural profiles of human miRNA families from pairwise clustering

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

The impact of target site accessibility on the design of effective siRNAs

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNAplex: a fast tool for RNA-RNA interaction search

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Efficient parameter estimation for RNA secondary structure prediction

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

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

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Local RNA base pairing probabilities in large sequences

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Prediction of locally stable RNA secondary structures for genome-wide surveys

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Prediction of RNA base pairing probabilities on massively parallel computers

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Automatic detection of conserved base pairing patterns in RNA virus genomes

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Statistics of RNA secondary structures

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

RNA multi-structure landscapes. A study based on temperature dependent partition functions

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

From sequences to shapes and back: a case study in RNA secondary structures

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

An improved algorithm for nucleic acid secondary structure display

29 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3319429

Nearest-neighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text]

29 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22115189

12 December 2020

inferred from PubMed ID database lookup

Physical aspects of evolutionary optimization and adaptation

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22115189

12 December 2020

inferred from PubMed ID database lookup

Statistics of landscapes based on free energies, replication and degradation rate constants of RNA secondary structures

1 reference

https://api.crossref.org/works/10.1186%2F1748-7188-6-26

7 January 2021

Fast folding and comparison of RNA secondary structures

1 reference

https://api.crossref.org/works/10.1186%2F1748-7188-6-26

7 January 2021

RNA secondary structures and their prediction

1 reference

https://api.crossref.org/works/10.1186%2F1748-7188-6-26

7 January 2021

Algorithm independent properties of RNA secondary structure predictions

1 reference

https://api.crossref.org/works/10.1186%2F1748-7188-6-26

7 January 2021

Barrier Trees of Degenerate Landscapes

1 reference

https://api.crossref.org/works/10.1186%2F1748-7188-6-26

7 January 2021

Identifiers

DOI

10.1186/1748-7188-6-26

1 reference

journals/almob/LorenzBSTFSH11

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions publication ID

28 January 2021

1 reference

9 September 2019

https://scigraph.springernature.com/pub.10.1186/1748-7188-6-26

1 reference

1 reference

PubMed publication ID

22115189

1 reference