PUBLICATION
Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs
- Authors
- Chou, M.T., Han, B.W., Hsiao, C.P., Zamore, P.D., Weng, Z., Hung, J.H.
- ID
- ZDB-PUB-170214-179
- Date
- 2015
- Source
- Nucleic acids research 43: e109 (Journal)
- Registered Authors
- Keywords
- none
- MeSH Terms
-
- Algorithms*
- Animals
- Arabidopsis/genetics
- Drosophila melanogaster/genetics
- HeLa Cells
- Humans
- MicroRNAs/chemistry*
- RNA, Small Interfering/chemistry*
- Sequence Alignment/methods*
- Sequence Analysis, RNA/methods*
- Software
- Zebrafish/genetics
- PubMed
- 26007652 Full text @ Nucleic Acids Res.
Citation
Chou, M.T., Han, B.W., Hsiao, C.P., Zamore, P.D., Weng, Z., Hung, J.H. (2015) Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic acids research. 43:e109.
Abstract
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.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping