Dataset Information

MIRPIPE: quantification of microRNAs in niche model organisms.

ABSTRACT:

Unlabelled

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.

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 Web site.

SUBMITTER: Kuenne C

PROVIDER: S-EPMC4816158 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Publications

MIRPIPE: quantification of microRNAs in niche model organisms.

Kuenne Carsten C Preussner Jens J Herzog Mario M Braun Thomas T Looso Mario M

Bioinformatics (Oxford, England) 20140826 23

<h4>Unlabelled</h4>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 ra ...[more]

PMID: 25165094

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Dataset Information

MIRPIPE: quantification of microRNAs in niche model organisms.

Unlabelled

Availability and implementation

Publications

MIRPIPE: quantification of microRNAs in niche model organisms.

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