TY  - JOUR
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
TI  - Oasis 2: improved online analysis of small RNA-seq data.
JO  - BMC bioinformatics
VL  - 19
IS  - 1
SN  - 1471-2105
CY  - Heidelberg
PB  - Springer
M1  - DZNE-2020-06119
SP  - 54
PY  - 2018
AB  - 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.
KW  - Base Sequence
KW  - Gene Expression Profiling
KW  - High-Throughput Nucleotide Sequencing
KW  - MicroRNAs: genetics
KW  - RNA, Small Untranslated: genetics
KW  - Sequence Analysis, RNA: methods
KW  - Software
KW  - Statistics as Topic: methods
KW  - MicroRNAs (NLM Chemicals)
KW  - RNA, Small Untranslated (NLM Chemicals)
LB  - PUB:(DE-HGF)16
C6  - pmid:29444641
C2  - pmc:PMC5813365
DO  - DOI:10.1186/s12859-018-2047-z
UR  - https://pub.dzne.de/record/139797
ER  -