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An online tool for analysing large amounts of small RNA-Seq data and acquiring their modifications profile. It allows the mapping of the input sequences to miRBase in order to decipher the miRNA expression content in the input samples. It also identifies any modifications related with the input sequences. The modification types that are being supported include all types of 3’-modifications (e.g. uridylation, adenylation, ADAR editing), 5’-modifications and also internal modifications (SNPs and ADARs). Chimira expects as an input FASTQ or FASTA files containing adapter and/or barcode stripped small RNA-Seq data.

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Chimira version 1.0
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  • Dimitrios M. Vitsios <dvitsios at ebi.ac.uk>


EMBL – European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

  • (Vitsios and Enright, 2015) Chimira: Analysis of small RNA Sequencing data and microRNA modifications. Bioinformatics.
    PMID: 26093149
  • (Li et al., 2012) Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis. Nucleic acids research.
    PMID: 22287634
  • (Liu et al., 2014) Identifying miRNAs, targets and functions. Briefings in bioinformatics.
    PMID: 23175680

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