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1. Computational tools for identifying RNA modification sites:
(1) m6A sites
iRNA-Methyl: a computational methods for identifying m6A sites in Saccharomyces cerevisiae.
m6Apred: a computational methods for identifying m6A sites in Saccharomyces cerevisiae.
MethyRNA: a computational methods for identifying m6A sites in Homo sapiens, Mus musculus.
iRNA(m6A)-PseDNC: a computational methods for identifying m6A sites in Saccharomyces cerevisiae, which is an updated version of iRNA-Methyl.
(2) ψ
iRNA-PseU: a computational methods for identifying the ψ sites in Homo sapiens, Mus musculus, Saccharomyces cerevisiae.
(3) Adenosine to Inosine
iRNA-AI: a computational methods for identifying Adenosine to Inosine editing sites in Homo sapiens.
(4) 2'-O-Methylation
iRNA-2OM: a computational methods for identifying 2'-O-methylation sites in Homo sapiens.
(5) 5-methylcytosine
iRNA-m5C: a computational methods for identifying the 5-methylcytosine sites in Homo sapiens, Mus musculus, Saccharomyces cerevisiae.
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2. Modomics: a database presents RNA modification pathways on the level of nucleosides.
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3. RNApathwaysDB: a databases deals with RNA metabolism with respect to whole RNA molecules.
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4. RMBase: a database integrates epitranscriptome sequencing data for the exploration of post-transcriptional modifications of RNAs and their relationships with miRNA binding events, disease-related single-nucleotide polymorphisms (SNPs) and RNA-binding proteins (RBPs).
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5. M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers.
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6. m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome.
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7. Whistle: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach.
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8. m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome.