Journal Article

DZNE-2020-06119

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Oasis 2: improved online analysis of small RNA-seq data.

Rahman, R.-U. (First author)DZNE* ; Gautam, A.DZNE* ; Bethune, J.DZNE* ; Sattar, A.DZNE* ; Fiosins, M.DZNE* ; Magruder, D. S.DZNE* ; Capece, V.DZNE* ; Shomroni, O.DZNE* ; Bonn, S. (Last author)DZNE*

2018
Springer Heidelberg

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Please use a persistent id in citations: doi:10.1186/s12859-018-2047-z

Abstract: Small RNA molecules play important roles in many biological processes and their dysregulation or dysfunction can cause disease. The current method of choice for genome-wide sRNA expression profiling is deep sequencing.Here we present Oasis 2, which is a new main release of the Oasis web application for the detection, differential expression, and classification of small RNAs in deep sequencing data. Compared to its predecessor Oasis, Oasis 2 features a novel and speed-optimized sRNA detection module that supports the identification of small RNAs in any organism with higher accuracy. Next to the improved detection of small RNAs in a target organism, the software now also recognizes potential cross-species miRNAs and viral and bacterial sRNAs in infected samples. In addition, novel miRNAs can now be queried and visualized interactively, providing essential information for over 700 high-quality miRNA predictions across 14 organisms. Robust biomarker signatures can now be obtained using the novel enhanced classification module.Oasis 2 enables biologists and medical researchers to rapidly analyze and query small RNA deep sequencing data with improved precision, recall, and speed, in an interactive and user-friendly environment.Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de.

Keyword(s): Base Sequence (MeSH) ; Gene Expression Profiling (MeSH) ; High-Throughput Nucleotide Sequencing (MeSH) ; MicroRNAs: genetics (MeSH) ; RNA, Small Untranslated: genetics (MeSH) ; Sequence Analysis, RNA: methods (MeSH) ; Software (MeSH) ; Statistics as Topic: methods (MeSH) ; MicroRNAs ; RNA, Small Untranslated

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Contributing Institute(s):

1. Computational analysis of biological networks (AG Bonn 1)
2. Computational Systems Biology (AG Bonn 2)
3. Epigenetics and Systems Medicine in Neurodegenerative Diseases (AG Fischer)

Research Program(s):

1. 342 - Disease Mechanisms and Model Systems (POF3-342) (POF3-342)

Appears in the scientific report 2018

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Database coverage:
; ; ; ; BIOSIS Previews ; Clarivate Analytics Master Journal List ; DOAJ Seal ; Ebsco Academic Search ; IF < 5 ; JCR ; SCOPUS ; Web of Science Core Collection

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