DANSR: A Tool for the Detection of Annotated and Novel Small RNAs.
DANSR: A Tool for the Detection of Annotated and Novel Small RNAs.
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DOI：
10.3390/ncrna8010009
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发表时间：
2022-01-13
期刊：
影响因子：
4.3
通讯作者：
Maher CA
中科院分区：
文献类型：
--
作者：
Zhang J;Eteleeb AM;Rozycki EB;Inkman MJ;Ly A;Scharf RE;Jayachandran K;Krasnick BA;Mazur T;White NM;Fields RC;Maher CA
现有的小非编码RNA分析工具经过优化，可以处理短测序reads（17-35个核苷酸）以监测microRNA的表达。然而，这些策略不足以代表36-200个核苷酸长度范围内的许多生物学相关的小非编码rna类别（trna， snorna等）。为了解决这个问题，我们开发了DANSR，这是一种使用可变长度（范围从17-200 nt）测序读段检测带注释和新型小rna的工具。虽然DANSR广泛适用于任何小RNA数据集，但我们将其应用于匹配的正常，原发性和远处转移性结直肠癌标本队列，以证明其量化注释小RNA，发现新基因和计算差异表达的能力。DANSR是一个开源工具。
Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17–35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36–200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17–200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool.
影响因子：
14.9
作者：
Ragan C;Mowry BJ;Bauer DC
通讯作者：
Bauer DC