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Keywords {🔍}

editing, rna, sites, pubmed, rnaseq, data, reads, article, fig, google, scholar, longread, lgiremi, cas, read, file, central, sequencing, additional, snps, method, atog, alu, mismatch, glm, regions, variants, human, methods, predicted, information, genome, long, allelespecific, high, analysis, identification, atoi, shortread, calculated, identified, short, score, strand, pairs, mismatches, datasets, nat, site, dataset,

Topics {✒️}

double-stranded-rna-specific adenosine deaminase long-read rna-seq yielded long-read rna-seq overcomes long-read rna-seq affords short-read rna-seq appeared long-read rna-seq data short-read rna-seq data endogenous double-stranded rnas short-read rna-seq analysis single-cell full-length isoforms short-read rna-seq methods double-stranded rna structures uncover allele-specific editing double-stranded rna prediction characterize full-length transcripts long-read rna-seq dsrna unwinding/modifying activity double-stranded rnas quantify full-length isoforms short-read rna-seq allele-specific rna editing rna editing primate-specific long-read bioinformatics tool allele-specific editing sites detecting allele-specific editing direct-zol™ rna miniprep pacbio rna-seq data quick-dna™ miniprep kit allele-specific editing event article download pdf allele-specific editing exists current long-read datasets long-read transcript sequences highly structured nature lps-stimulated immune cells alter protein-coding sequences full-length transcript characterization read-specific editing ratio final l-giremi predictions �pseudo-genome-aware” approach sample-specific genomic variations analyze single-nucleotide variants l-giremi algorithm consists pseudo-genome-aware method actual editing profiles rna editing analyses traditional “genome-aware” methods full size image full-length transcriptome identification sample-specific genomic data

Questions {❓}

• Is abundant A-to-I RNA editing primate-specific?

Schema {🗺️}

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         description:Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors and read biases. Applied to PacBio RNA-seq data, L-GIREMI affords a high accuracy in RNA editing identification. Additionally, our analysis uncovered novel insights about RNA editing occurrences in single molecules and double-stranded RNA structures. L-GIREMI provides a valuable means to study nucleotide variants in long-read RNA-seq.
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            Double-stranded RNA
            Mutual information
            Animal Genetics and Genomics
            Human Genetics
            Plant Genetics and Genomics
            Microbial Genetics and Genomics
            Bioinformatics
            Evolutionary Biology
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      headline:L-GIREMI uncovers RNA editing sites in long-read RNA-seq
      description:Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors and read biases. Applied to PacBio RNA-seq data, L-GIREMI affords a high accuracy in RNA editing identification. Additionally, our analysis uncovered novel insights about RNA editing occurrences in single molecules and double-stranded RNA structures. L-GIREMI provides a valuable means to study nucleotide variants in long-read RNA-seq.
      datePublished:2023-07-20T00:00:00Z
      dateModified:2023-07-20T00:00:00Z
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         A-to-I editing
         Double-stranded RNA
         Mutual information
         Animal Genetics and Genomics
         Human Genetics
         Plant Genetics and Genomics
         Microbial Genetics and Genomics
         Bioinformatics
         Evolutionary Biology
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      name:Department of Integrative Biology and Physiology, University of California, Los Angeles, USA
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      name:Bioinformatics Interdepartmental Program, University of California, Los Angeles, USA

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