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Bioinformatics. 2013 Oct 15;29(20):2651-2. doi: 10.1093/bioinformatics/btt457. Epub 2013 Aug 13.

omiRas: a Web server for differential expression analysis of miRNAs derived from small RNA-Seq data.

Author information

1
Plant Molecular Biology, Institute of Molecular BioSciences, University of Frankfurt am Main, Marie-Curie-Str.9, 60439 Frankfurt am Main, GenXPro GmbH, Frankfurt Innovation Center Biotechnology, Altenhöferallee 3, 60438 Frankfurt am Main and Molecular Bioinformatics Group, Institute of Computer Science, Faculty of Computer Science and Mathematics, Cluster of Excellence, Frankfurt "Macromolecular Complexes", Robert-Mayer-Strasse 11-15, 60325 Frankfurt am Main, Germany.

Abstract

SUMMARY:

Small RNA deep sequencing is widely used to characterize non-coding RNAs (ncRNAs) differentially expressed between two conditions, e.g. healthy and diseased individuals and to reveal insights into molecular mechanisms underlying condition-specific phenotypic traits. The ncRNAome is composed of a multitude of RNAs, such as transfer RNA, small nucleolar RNA and microRNA (miRNA), to name few. Here we present omiRas, a Web server for the annotation, comparison and visualization of interaction networks of ncRNAs derived from next-generation sequencing experiments of two different conditions. The Web tool allows the user to submit raw sequencing data and results are presented as: (i) static annotation results including length distribution, mapping statistics, alignments and quantification tables for each library as well as lists of differentially expressed ncRNAs between conditions and (ii) an interactive network visualization of user-selected miRNAs and their target genes based on the combination of several miRNA-mRNA interaction databases.

AVAILABILITY AND IMPLEMENTATION:

The omiRas Web server is implemented in Python, PostgreSQL, R and can be accessed at: http://tools.genxpro.net/omiras/.

PMID:
23946503
DOI:
10.1093/bioinformatics/btt457
[Indexed for MEDLINE]

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