PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation. (Q41966757)

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scientific article published on 10 January 2013

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English	PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation.	scientific article published on 10 January 2013

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scholarly article

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23 February 2020

PREPACT 2.0: Predicting C-to-U and U-to-C RNA Editing in Organelle Genome Sequences with Multiple References and Curated RNA Editing Annotation (English)

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23 February 2020

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23 February 2020

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Volker Knoop

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23 February 2020

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10 January 2013

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23 February 2020

Bioinformatics and Biology Insights

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23 February 2020

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23 February 2020

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23 February 2020

A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

Evolutionary origin of RNA editing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

A complete sequence and transcriptomic analyses of date palm (Phoenix dactylifera L.) mitochondrial genome

1 reference

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5 June 2018

Plant-type mitochondrial RNA editing in the protist Naegleria gruberi

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

The mitochondrial genomes of the early land plants Treubia lacunosa and Anomodon rugelii: dynamic and conservative evolution

1 reference

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5 June 2018

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA.

1 reference

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5 June 2018

Extreme RNA Editing in Coding Islands and Abundant Microsatellites in Repeat Sequences of Selaginella moellendorffii Mitochondria: The Root of Frequent Plant mtDNA Recombination in Early Tracheophytes

1 reference

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5 June 2018

A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

When you can’t trust the DNA: RNA editing changes transcript sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: selection vs. retroprocessing as the driving force

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing

1 reference

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5 June 2018

Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

Introducing the plant RNA editing prediction and analysis computer tool PREPACT and an update on RNA editing site nomenclature

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

CURE-Chloroplast: a chloroplast C-to-U RNA editing predictor for seed plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

REDIdb: the RNA editing database.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

Genetic algorithm learning as a robust approach to RNA editing site prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

Editing of plastid RNA in Arabidopsis thaliana ecotypes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

PREP-Mt: predictive RNA editor for plant mitochondrial genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

A pentatricopeptide repeat protein is essential for RNA editing in chloroplasts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

Simple statistical models predict C-to-U edited sites in plant mitochondrial RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

RNA editing in hornwort chloroplasts makes more than half the genes functional

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

The Plastid Chromosome of Atropa belladonna and its Comparison with that of Nicotiana tabacum: The Role of RNA Editing in Generating Divergence in the Process of Plant Speciation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

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=3547502

5 June 2018

Creation of a novel protein-coding region at the RNA level in black pine chloroplasts: the pattern of RNA editing in the gymnosperm chloroplast is different from that in angiosperms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

Major transcript of the frameshifted coxII gene from trypanosome mitochondria contains four nucleotides that are not encoded in the DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

5 June 2018

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=3547502

5 June 2018

Nuclear DYW-type PPR gene families diversify with increasing RNA editing frequencies in liverwort and moss mitochondria

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

DYW-type PPR proteins in a heterolobosean protist: plant RNA editing factors involved in an ancient horizontal gene transfer?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

A DYW domain-containing pentatricopeptide repeat protein is required for RNA editing at multiple sites in mitochondria of Arabidopsis thaliana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

Prediction of C-to-U RNA editing sites in plant mitochondria using both biochemical and evolutionary information

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

Prediction of C-to-U RNA editing sites in higher plant mitochondria using only nucleotide sequence features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

Evolution of a pseudogene: exclusive survival of a functional mitochondrial nad7 gene supports Haplomitrium as the earliest liverwort lineage and proposes a secondary loss of RNA editing in Marchantiidae

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

High levels of RNA editing in a vascular plant chloroplast genome: analysis of transcripts from the fern Adiantum capillus-veneris.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

Tissue- and stage-specific RNA editing of rps 14 transcripts in moss (Physcomitrella patens) chloroplasts

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

Identification of RNA editing sites in chloroplast transcripts from the maternal and paternal progenitors of tobacco (Nicotiana tabacum): comparative analysis shows the involvement of distinct trans-factors for ndhB editing.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

RNA editing sites in tobacco chloroplast transcripts: editing as a possible regulator of chloroplast RNA polymerase activity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

An ancestral mitochondrial DNA resembling a eubacterial genome in miniature

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

18 August 2018

A hypothesis on the identification of the editing enzyme in plant organelles

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3547502

2 December 2018

Conservation of RNA editing between rice and maize plastids: are most editing events dispensable?

1 reference

https://pubmed.ncbi.nlm.nih.gov/23362369

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Comparative analysis of RNA editing sites in higher plant chloroplasts

1 reference

https://pubmed.ncbi.nlm.nih.gov/23362369

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Chloroplast ribosomal S14 protein transcript is edited to create a translation initiation codon in the moss Physcomitrella patens

1 reference

https://pubmed.ncbi.nlm.nih.gov/23362369

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

A systematic search for RNA editing sites in pea chloroplasts: an editing event causes diversification from the evolutionarily conserved amino acid sequence

1 reference

https://pubmed.ncbi.nlm.nih.gov/23362369

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Characterization of the complete chloroplast genome of Hevea brasiliensis reveals genome rearrangement, RNA editing sites and phylogenetic relationships

1 reference

https://pubmed.ncbi.nlm.nih.gov/23362369

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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10.4137/BBI.S11059

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23362369%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

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Europe PubMed Central

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23 February 2020

PubMed publication ID

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Europe PubMed Central

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:23362369%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

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