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          Institute: MPI für Herz- und Lungenforschung (W. G. Kerckhoff Institut)     Collection: Yearbook_2015     Display Documents



ID: 711893.0, MPI für Herz- und Lungenforschung (W. G. Kerckhoff Institut) / Yearbook_2015
MIRPIPE: quantification of microRNAs in niche model organisms
Authors:Kuenne, C.; Preussner, J.; Herzog, M.; Braun, T.; Looso, M.
Date of Publication (YYYY-MM-DD):2014-12-01
Title of Journal:Bioinformatics
Volume:30
Issue / Number:23
Start Page:3412
End Page:3413
Audience:Not Specified
Abstract / Description: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.
Free Keywords:Algorithms; Humans; MicroRNAs/*chemistry; Models, Biological; Sequence Analysis, RNA/*methods; *Software
External Publication Status:published
Document Type:Article
Communicated by:MPI für Herz- und Lungenforschung
Affiliations:MPI für physiologische und klinische Forschung
External Affiliations:%^ 1435822261
Identifiers:ISSN:1367-4811 (Electronic) 1367-4803 (Linking) %R 10.1093/bioinformatics/btu573
URL:http://www.ncbi.nlm.nih.gov/pubmed/25165094
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