scholarly journals Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

RNA ◽  
2009 ◽  
Vol 15 (12) ◽  
pp. 2147-2160 ◽  
Author(s):  
C. Cole ◽  
A. Sobala ◽  
C. Lu ◽  
S. R. Thatcher ◽  
A. Bowman ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rnas ◽  
Sequencing Data ◽  
Deep Sequencing Data

scholarly journals Oasis2.0: improved online analysis of small RNA-seq data

2017 ◽  
Author(s):  
Raza-Ur Rahman ◽  
Abhivyakti Gautam ◽  
Jörn Bethune ◽  
Abdul Sattar ◽  
Maksims Fiosins ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rna ◽  
Small Rnas ◽  
Web Application ◽  
The Novel ◽  
Sequencing Data ◽  
Essential Information ◽  
Deep Sequencing Data ◽  
Small Rna Deep Sequencing ◽  
User Friendly

AbstractOasis 2 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.Availability and Implementation: Oasis 2 is implemented in Java, J2EE, mysql, Python, R, PHP and JavaScript. It is freely available at http://oasis.dzne.de

scholarly journals deepBase v2.0: identification, expression, evolution and function of small RNAs, LncRNAs and circular RNAs from deep-sequencing data

2015 ◽  
Vol 44 (D1) ◽  
pp. D196-D202 ◽  
Author(s):  
Ling-Ling Zheng ◽  
Jun-Hao Li ◽  
Jie Wu ◽  
Wen-Ju Sun ◽  
Shun Liu ◽  
...  
Keyword(s):  
Deep Sequencing ◽  
Small Rnas ◽  
Circular Rnas ◽  
Sequencing Data ◽  
Deep Sequencing Data ◽  
Expression Evolution ◽  
And Function

scholarly journals GenomeGems: evaluation of genetic variability from deep sequencing data

2012 ◽  
Vol 5 (1) ◽  
pp. 338
Author(s):  
Sharon Ben-Zvi ◽  
Adi Givati ◽  
Noam Shomron
Keyword(s):  
Genetic Variability ◽  
Deep Sequencing ◽  
Sequencing Data ◽  
Deep Sequencing Data

Considering DNA damage when interpreting mtDNA heteroplasmy in deep sequencing data

2017 ◽  
Vol 26 ◽  
pp. 1-11 ◽  
Author(s):  
Molly M. Rathbun ◽  
Jennifer A. McElhoe ◽  
Walther Parson ◽  
Mitchell M. Holland
Keyword(s):  
Dna Damage ◽  
Deep Sequencing ◽  
Sequencing Data ◽  
Deep Sequencing Data

scholarly journals Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data

Biology ◽  
2012 ◽  
Vol 1 (2) ◽  
pp. 297-310 ◽  
Author(s):  
Xiaozeng Yang ◽  
Lei Li
Keyword(s):  
Deep Sequencing ◽  
Sequencing Data ◽  
Deep Sequencing Data

scholarly journals Discovery of Novel Human Breast Cancer MicroRNAs from Deep Sequencing Data by Analysis of Pri-MicroRNA Secondary Structures

PLoS ONE ◽  
2011 ◽  
Vol 6 (2) ◽  
pp. e16403 ◽  
Author(s):  
Seongho Ryu ◽  
Natasha Joshi ◽  
Kevin McDonnell ◽  
Jongchan Woo ◽  
Hyejin Choi ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Deep Sequencing ◽  
Human Breast Cancer ◽  
Secondary Structures ◽  
Human Breast ◽  
Sequencing Data ◽  
Deep Sequencing Data
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