Oasis 2: improved online analysis of small RNA-seq data
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Oasis 2: improved online analysis of small RNA-seq data. / Rahman, Raza-Ur; Gautam, Abhivyakti; Bethune, Jörn; Sattar, Abdul; Fiosins, Maksims; Magruder, Daniel Sumner; Capece, Vincenzo; Shomroni, Orr; Bonn, Stefan.
in: BMC BIOINFORMATICS, Jahrgang 19, Nr. 1, 14.02.2018, S. 54.Publikationen: SCORING: Beitrag in Fachzeitschrift/Zeitung › SCORING: Zeitschriftenaufsatz › Forschung › Begutachtung
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TY - JOUR
T1 - Oasis 2: improved online analysis of small RNA-seq data
AU - Rahman, Raza-Ur
AU - Gautam, Abhivyakti
AU - Bethune, Jörn
AU - Sattar, Abdul
AU - Fiosins, Maksims
AU - Magruder, Daniel Sumner
AU - Capece, Vincenzo
AU - Shomroni, Orr
AU - Bonn, Stefan
PY - 2018/2/14
Y1 - 2018/2/14
N2 - BACKGROUND: 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.RESULTS: 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.CONCLUSIONS: 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.AVAILABILITY AND IMPLEMENTATION: Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de.
AB - BACKGROUND: 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.RESULTS: 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.CONCLUSIONS: 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.AVAILABILITY AND IMPLEMENTATION: Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at https://oasis.dzne.de.
KW - Base Sequence
KW - Gene Expression Profiling
KW - High-Throughput Nucleotide Sequencing
KW - MicroRNAs
KW - RNA, Small Untranslated
KW - Sequence Analysis, RNA
KW - Software
KW - Statistics as Topic
KW - Journal Article
KW - Research Support, Non-U.S. Gov't
U2 - 10.1186/s12859-018-2047-z
DO - 10.1186/s12859-018-2047-z
M3 - SCORING: Journal article
C2 - 29444641
VL - 19
SP - 54
JO - BMC BIOINFORMATICS
JF - BMC BIOINFORMATICS
SN - 1471-2105
IS - 1
ER -