BlastR--fast and accurate database searches for non-coding RNAs (Q35198308)

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English	BlastR--fast and accurate database searches for non-coding RNAs	scientific article

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scholarly article

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Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

title

BlastR--fast and accurate database searches for non-coding RNAs (English)

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Europe PubMed Central

PubMed publication ID

21624887

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7 August 2017

main subject

database

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author

Cedric Notredame

series ordinal

8

object named as

Cedric Notredame

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Giovanni Bussotti

object named as

Giovanni Bussotti

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1

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Andreas Wilm

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Andreas Wilm

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5

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Ionas Erb

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Ionas Erb

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3

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author name string

Emanuele Raineri

series ordinal

2

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stated in

Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

Matthias Zytnicki

series ordinal

4

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stated in

Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

Emmanuel Beaudoing

series ordinal

6

1 reference

stated in

Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

Philipp Bucher

series ordinal

7

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stated in

Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

language of work or name

English

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publication date

30 May 2011

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Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

published in

Nucleic Acids Research

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stated in

Europe PubMed Central

PubMed publication ID

21624887

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7 August 2017

volume

39

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stated in

Europe PubMed Central

PubMed publication ID

21624887

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7 August 2017

issue

16

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stated in

Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

page(s)

6886-6895

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stated in

Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

copyright license

Creative Commons Attribution-NonCommercial 3.0 Unported

start time

7 November 2016

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stated in

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Long noncoding RNAs with enhancer-like function in human cells

1 reference

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PubMed Central

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13 July 2018

The tedious task of finding homologous noncoding RNA genes

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13 July 2018

The use of covariance models to annotate RNAs in whole genomes

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PubMed Central

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13 July 2018

Relative mutation rates of each nucleotide for another estimated from allele frequency spectra at human gene loci

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13 July 2018

Infernal 1.0: inference of RNA alignments

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13 July 2018

Evolution and functions of long noncoding RNAs

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13 July 2018

Sequence context-specific profiles for homology searching

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13 July 2018

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

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13 July 2018

Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues

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13 July 2018

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities

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PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

The Pfam protein families database

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13 July 2018

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs

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PubMed Central

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13 July 2018

Considerations in the identification of functional RNA structural elements in genomic alignments

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PubMed Central

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13 July 2018

Exploring genomic dark matter: a critical assessment of the performance of homology search methods on noncoding RNA

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PubMed Central

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13 July 2018

Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints

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PubMed Central

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13 July 2018

Comprehensive thermodynamic analysis of 3' double-nucleotide overhangs neighboring Watson-Crick terminal base pairs

1 reference

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PubMed Central

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13 July 2018

A distinct small RNA pathway silences selfish genetic elements in the germline

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PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

Sequence-based heuristics for faster annotation of non-coding RNA families.

1 reference

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PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

A strategy for probing the function of noncoding RNAs finds a repressor of NFAT

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PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

The transcriptional landscape of the mammalian genome

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PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

Rfam: annotating non-coding RNAs in complete genomes

1 reference

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PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

RALEE--RNA ALignment editor in Emacs

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PubMed Central

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13 July 2018

RSEARCH: finding homologs of single structured RNA sequences

1 reference

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PubMed Central

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

13 July 2018

Rfam: an RNA family database

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

A greedy algorithm for aligning DNA sequences

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

Profile hidden Markov models

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

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13 July 2018

RAGA: RNA sequence alignment by genetic algorithm

1 reference

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PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

13 July 2018

Mammalian gene evolution: nucleotide sequence divergence between mouse and rat

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

13 July 2018

RNA sequence analysis using covariance models

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

13 July 2018

Basic local alignment search tool

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

13 July 2018

Amino acid substitution matrices from protein blocks

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

13 July 2018

A sequence-based filtering method for ncRNA identification and its application to searching for riboswitch elements.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

26 September 2018

The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

26 September 2018

Empirical models for substitution in ribosomal RNA.

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

26 September 2018

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

1 reference

stated in

PubMed Central

reference URL

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3167602

retrieved

26 September 2018

Identifiers

DOI

10.1093/NAR/GKR335

1 reference

stated in

Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

PMC publication ID

3167602

1 reference

stated in

Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

PubMed publication ID

21624887

1 reference

stated in

Europe PubMed Central

PubMed publication ID

21624887

retrieved

7 August 2017

ResearchGate publication ID

51176967

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