標題: Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
作者: Chou, Min-Te
Han, Bo W.
Hsiao, Chiung-Po
Zamore, Phillip D.
Weng, Zhiping
Hung, Jui-Hung
生物科技學系
生物資訊及系統生物研究所
Department of Biological Science and Technology
Institude of Bioinformatics and Systems Biology
公開日期: 30-九月-2015
摘要: Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3' end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor.
URI: http://dx.doi.org/10.1093/nar/gkv537
http://hdl.handle.net/11536/129596
ISSN: 0305-1048
DOI: 10.1093/nar/gkv537
期刊: NUCLEIC ACIDS RESEARCH
Volume: 43
Issue: 17
起始頁: 0
結束頁: 0
顯示於類別:期刊論文


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