(Q24644581)

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De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18347326%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: performance of Markov-dependent genome feature scoring (English)

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18347326%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

Dictyostelium discoideum

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1

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4 January 2020

author name string

Andrea Hinas

2

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4 January 2020

David H Ardell

3

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4 January 2020

Leif A Kirsebom

4

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4 January 2020

Anders Virtanen

5

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4 January 2020

Fredrik Söderbom

6

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4 January 2020

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17 March 2008

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4 January 2020

Genome Research

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4 January 2020

18

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4 January 2020

6

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4 January 2020

888-899

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Europe PubMed Central

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4 January 2020

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

1 reference

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7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Experimental approaches to identify non-coding RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

dictyBase, the model organism database for Dictyostelium discoideum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

A computational screen for mammalian pseudouridylation guide H/ACA RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Silencing of retrotransposons in Dictyostelium by DNA methylation and RNAi

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

The genome of the social amoeba Dictyostelium discoideum

1 reference

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7 April 2017

Structural implications of novel diversity in eucaryal RNase P RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

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=2413156

7 April 2017

Rfam: annotating non-coding RNAs in complete genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Novel non-coding RNAs in Dictyostelium discoideum and their expression during development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Genome sequence of the human malaria parasite Plasmodium falciparum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Noncoding RNA genes identified in AT-rich hyperthermophiles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

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=2413156

7 April 2017

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Basic local alignment search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

Secondary structure prediction 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=2413156

7 April 2017

Spliceosomal UsnRNP biogenesis, structure and function

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

A computational screen for methylation guide snoRNAs in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 April 2017

A kingdom-level phylogeny of eukaryotes based on combined protein data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

7 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=2413156

7 April 2017

AT excursion: a new approach to predict replication origins in viral genomes by locating AT-rich regions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

27 September 2017

A practical guide to the art of RNA gene prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

27 September 2017

Treasure hunt in an amoeba: non-coding RNAs in Dictyostelium discoideum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

27 September 2017

Identification of the major spliceosomal RNAs in Dictyostelium discoideum reveals developmentally regulated U2 variants and polyadenylated snRNAs.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

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=2413156

27 September 2017

Identification and characterization of small RNAs involved in RNA silencing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

27 September 2017

Sequence and structure of the extrachromosomal palindrome encoding the ribosomal RNA genes in Dictyostelium.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

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=2413156

27 September 2017

Searching for RNA genes using base-composition statistics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

27 September 2017

The complex repeats of Dictyostelium discoideum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

27 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

27 September 2017

Dinucleotide relative abundance extremes: a genomic signature

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

27 September 2017

Developmental regulation of Dictyostelium discoideum actin gene fusions carried on low-copy and high-copy transformation vectors

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

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=2413156

27 September 2017

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

30 May 2018

Chance and statistical significance in protein and DNA sequence analysis.

1 reference

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30 May 2018

Cultivation and synchronous morphogenesis of Dictyostelium under controlled experimental conditions.

1 reference

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19 June 2018

Maximum-scoring segment sets.

1 reference

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28 November 2018

U1-like snRNAs lacking complementarity to canonical 5' splice sites.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

28 November 2018

A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A-T rich genome of Plasmodium falciparum

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

28 November 2018

Selenocysteine tRNA identification in the model organisms Dictyostelium discoideum and Tetrahymena thermophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

28 November 2018

A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction

1 reference

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28 November 2018

RnaViz 2: an improved representation of RNA secondary structure.

1 reference

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28 November 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2413156

28 November 2018

Comparative DNA analysis across diverse genomes.

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28 November 2018

The small nuclear RNAs of the cellular slime mold Dictyostelium discoideum. Isolation and characterization

1 reference

https://pubmed.ncbi.nlm.nih.gov/18347326

12 December 2020

based on heuristic

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10.1101/GR.069104.107

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Consolidated OpenCitations Corpus – April 2017

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4 January 2020

OpenCitations bibliographic resource ID

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Consolidated OpenCitations Corpus – April 2017

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2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18347326%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

PubMed publication ID

2 references

Consolidated OpenCitations Corpus – April 2017

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18347326%20AND%20SRC:MED&resulttype=core&format=json

4 January 2020

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