Tailor – a computational framework for detecting non-templated tailing of small silencing RNAs

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.

A team from National Chiao Tung University and the University of Massachusetts Medical School has 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.

rna-seqBWT-based tailing detection algorithm. (A) Procedure of constructing the FM-index from a reference sequence. (B) Procedure of query searching using the FM-index. Searching starts from the 3′ end of a reverse-complemented query. Green letters indicate the non-templated tail. Red letters indicate the positions being matched against the index. When a non-templated letter is spotted as in step 4, the algorithm backtracks to previous step and reports all the hits and marks the unmatched string as ‘tail’.

Availability – The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor

Chou MT, Han BW, Hsiao CP, Zamore PD, Weng Z, Hung JH. (2015) Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic Acids Res [Epub ahead of print]. [article]

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