MIRPIPE – quantification of microRNAs in niche model organisms

MicroRNAs represent an important class of small non-coding RNAs regulating gene expression in eukaryotes. Present algorithms typically rely on genomic data to identify miRNAs and require extensive installation procedures. Niche model organisms lacking genomic sequences cannot be analyzed by such tools. Here researchers from the Max Planck Institute for Heart and Lung Research introduce the MIRPIPE application enabling rapid and simple browser-based miRNA homology detection and quantification. MIRPIPE features automatic trimming of raw RNA-Seq reads originating from various sequencing instruments, processing of isomiRs, and quantification of detected miRNAs versus public or user uploaded reference databases.

rna-seq

 Availability and Implementation: The web service is freely available at http://bioinformatics.mpi-bn.mpg.de

MIRPIPE was implemented in Perl and integrated into Galaxy. An offline version for local execution is also available from our website.

Contact: Mario.Looso@mpi-bn.mpg.de

Kuenne C, Preussner J, Herzog M, Braun T, Looso M. (2014) MIRPIPE – quantification of microRNAs in niche model organisms. Bioinformatics [Epub ahead of print]. [article]