FindNonCoding: rapid and simple detection of non-coding RNAs in genomes

Non-coding RNAs are often neglected during genome annotation due to their difficulty of detection relative to protein coding genes. FindNonCoding takes a pattern mining approach to capture the essential sequence motifs and hairpin loops representing a non-coding RNA family and quickly identify matches in genomes. FindNonCoding was designed for ease of use and accurately finds non-coding RNAs with a low false discovery rate. Availability and implementation: FindNonCoding is implemented within the DECIPHER package (v2.19.3) for R (v4.1) available from Bioconductor. Pre-trained models of common non-coding RNA families are included for bacteria, archaea and eukarya.