RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs (Q36060804)

11 August 2017

RNASTAR: an RNA STructural Alignment Repository that provides insight into the evolution of natural and artificial RNAs (English)

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11 August 2017

13

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11 August 2017

Paul Gardner

5

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Catherine A. Lozupone

8

object named as

Catherine A Lozupone

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11 August 2017

3

Daniel McDonald

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11 August 2017

2

Jesse Stombaugh

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11 August 2017

Jeremy Widmann

1

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11 August 2017

Jana Chocholousova

4

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11 August 2017

Matthew K Iyer

6

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11 August 2017

Zongzhi Liu

7

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11 August 2017

John Quinn

9

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11 August 2017

Sandra Smit

10

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11 August 2017

Shandy Wikman

11

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11 August 2017

Jesse R R Zaneveld

12

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11 August 2017

language of work or name

English

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publication date

29 May 2012

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11 August 2017

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11 August 2017

18

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11 August 2017

7

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11 August 2017

1319-1327

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Boulder ALignment Editor (ALE): a web-based RNA alignment tool

11 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Infernal 1.0: inference of RNA alignments

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Frequency and isostericity of RNA base pairs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

tRNAdb 2009: compilation of tRNA sequences and tRNA genes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

The annotation of RNA motifs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Phylogeny-aware gap placement prevents errors in sequence alignment and evolutionary analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

FR3D: finding local and composite recurrent structural motifs in RNA 3D structures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Evolutionary rates vary among rRNA structural elements

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

The architectonics of programmable RNA and DNA nanostructures

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Natural selection is not required to explain universal compositional patterns in rRNA secondary structure categories

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

In vitro RNA random pools are not structurally diverse: a computational analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

A benchmark of multiple sequence alignment programs upon structural RNAs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

MUSCLE: multiple sequence alignment with high accuracy and high throughput

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Rfam: an RNA family database

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

The Neurospora Varkud satellite ribozyme

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

The non-Watson-Crick base pairs and their associated isostericity matrices

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Evidence for strong selective constraint acting on the nucleotide composition of 16S ribosomal RNA genes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Geometric nomenclature and classification of RNA base pairs

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Peptidyl transferase: ancient and exiguous

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Mutational study reveals that tertiary interactions are conserved in ribosomal frameshifting pseudoknots of two luteoviruses

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Conserved geometrical base-pairing patterns in RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Specific mutations in a viral RNA pseudoknot drastically change ribosomal frameshifting efficiency

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Tertiary Motifs in RNA Structure and Folding

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Specific binding of aminoglycoside antibiotics to RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Interlocking structural motifs mediate molecular discrimination by a theophylline-binding RNA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Saccharide-RNA recognition in an aminoglycoside antibiotic-RNA aptamer complex

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

RNA molecules that specifically and stoichiometrically bind aminoglycoside antibiotics with high affinities

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Structural basis of RNA folding and recognition in an AMP-RNA aptamer complex

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Structural basis of ligand discrimination by two related RNA aptamers resolved by NMR spectroscopy

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

In vitro selection analysis of neomycin binding RNAs with a mutagenized pool of variants of the 16S rRNA decoding region

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

High-resolution molecular discrimination by RNA.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

The RNA structure alignment ontology

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

RNA structure prediction from evolutionary patterns of nucleotide composition

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Alignment uncertainty and genomic analysis

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

A small catalytic RNA motif with Diels-Alderase activity.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Sequence-based identification of 3D structural modules in RNA with RMDetect

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Structural constraints and mutational bias in the evolutionary restoration of a severe deletion in RNA phage MS2.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Functional requirements for specific ligand recognition by a biotin-binding RNA pseudoknot

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Nucleotide sequence requirements for self-cleavage of Neurospora VS RNA.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3383963

Folding and catalysis by the VS ribozyme

23 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22645380

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A novel RNA motif for neomycin recognition

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22645380

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Properties of an in vitro selected Pb2+ cleavage motif

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22645380

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1261/RNA.032052.111

1 reference

11 August 2017

1 reference

11 August 2017

PubMed publication ID

22645380

1 reference