REDO: RNA Editing Detection in Plant Organelles Based on Variant Calling Results
| Autor: | Ibrahim O. Alanazi, Hasan Awad Aljohi, Qiang Lin, Jun Yu, Wanfei Liu, Songnian Hu, Sarah A. Alromaih, Shuangyang Wu |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Cocos Arabidopsis Computational biology Biology Genome Genome variation 03 medical and health sciences Genetics Molecular Biology computer.programming_language Plant Proteins Organelles Variant Call Format 030102 biochemistry & molecular biology Computational Biology Genetic Variation High-Throughput Nucleotide Sequencing Computational Mathematics 030104 developmental biology Computational Theory and Mathematics RNA editing RNA Plant Modeling and Simulation RNA Editing Perl computer Software |
| Zdroj: | Journal of computational biology : a journal of computational molecular cell biology. 25(5) |
| ISSN: | 1557-8666 |
| Popis: | RNA editing is a post-transcriptional or cotranscriptional process that changes the sequence of the precursor transcript by substitutions, insertions, or deletions. Almost all of the land plants undergo RNA editing in organelles (plastids and mitochondria). Although several software tools have been developed to identify RNA editing events, there has been a great challenge to distinguish true RNA editing events from genome variation, sequencing errors, and other factors. Here we introduce REDO, a comprehensive application tool for identifying RNA editing events in plant organelles based on variant call format files from RNA-sequencing data. REDO is a suite of Perl scripts that illustrate a bunch of attributes of RNA editing events in figures and tables. REDO can also detect RNA editing events in multiple samples simultaneously and identify the significant differential proportion of RNA editing loci. Comparing with similar tools, such as REDItools, REDO runs faster with higher accuracy, and more specificity at the cost of slightly lower sensitivity. Moreover, REDO annotates each RNA editing site in RNAs, whereas REDItools reports only possible RNA editing sites in genome, which need additional steps to obtain RNA editing profiles for RNAs. Overall, REDO can identify potential RNA editing sites easily and provide several functions such as detailed annotations, statistics, figures, and significantly differential proportion of RNA editing sites among different samples. |
| Databáze: | OpenAIRE |
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