title: MIRPIPE: quantification of microRNAs in niche model organisms.
abstract: MicroRNAs (miRNAs) 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 we 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.
  
  
  METHODS
  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 Web site.
authors.affiliation: Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, D-61231 Bad Nauheim, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Kuenne
authors.affiliation: Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, D-61231 Bad Nauheim, Germany.
authors.forename: Jens
authors.initials: J
authors.lastname: Preussner
authors.affiliation: Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, D-61231 Bad Nauheim, Germany.
authors.forename: Mario
authors.initials: M
authors.lastname: Herzog
authors.affiliation: Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, D-61231 Bad Nauheim, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Braun
authors.affiliation: Group of Bioinformatics and Cardiac Development and Remodelling, Max Planck Institute for Heart and Lung Research, Ludwigstrasse 43, D-61231 Bad Nauheim, Germany.
authors.forename: Mario
authors.initials: M
authors.lastname: Looso
mesh_terms: D000465:Algorithms; D006801:Humans; D035683:MicroRNAs / Q000737:chemistry*; D008954:Models, Biological; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs