miRkwood: a tool for the reliable identification of microRNAs in plant genomes.

Background: MicroRNAs (miRNAs) play crucial roles in post-transcriptional regulation of eukaryotic gene expression and are involved in many aspects of plant development. Although several prediction tools are available for metazoan genomes, the number of tools dedicated to plants is relatively limited.

Results: Here, we present miRkwood, a user-friendly tool for the identification of miRNAs in plant genomes using small RNA sequencing data.

Deciphering metatranscriptomic data.

Metatranscriptomic data contributes another piece of the puzzle to understanding the phylogenetic structure and function of a community of organisms. High-quality total RNA is a bountiful mixture of ribosomal, transfer, messenger and other noncoding RNAs, where each family of RNA is vital to answering questions concerning the hidden microbial world. Software tools designed for deciphering metatranscriptomic data fall under two main categories: the first is to reassemble millions of short nucleotide fragments produced by high-throughput sequencing technologies into the original full-length transcriptomes for all organisms within a sample, and the second is to taxonomically classify the organisms and determine their individual functional roles within a community.