Section: New Software and Platforms
Keywords: Bioinformatics - Genomics
miRkwood is a bioinformatic pipeline that allows for the fast and easy identification of microRNAs in plant genomes. It is both available as a webserver and a stand-alone software. It offers an user-friendly interface to navigate in the data, as well as many export options to allow the user to conduct further analyses on a local computer.
The method takes as input a set of small reads, that have been previously trimmed and aligned onto the reference genome. It identifies novel microRNAs on the basis of the distributions of reads and the potential of flanking genomic sequence to fold into a stem-loop secondary structure. Then the result is refined through a variety of additional complementary features that bring new evidence to the prediction: duplex stability, thermodynamic stability, phylogenetic conservation, repeats, etc.