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DOE OSTI · 1827219

tSFM 1.0: tRNA Structure–Function Mapper

Lawrence, Travis J.·Hadi-Nezhad, Fatemeh·Grosse, Ivo·Ardell, David H.
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Abstract

Structure-conditioned information statistics have proven useful to predict and visualize tRNA Class-Informative Features (CIFs) and their evolutionary divergences. Although permutation P-values can quantify the significance of CIF divergences between two taxa, their naive Monte Carlo approximation is slow and inaccurate. The Peaks-over-Threshold approach of Knijnenburg et al. (2009) promises improvements to both speed and accuracy of permutation P-values, but has no publicly available API. Here, we present tRNA Structure–Function Mapper (tSFM) v1.0, an open-source, multi-threaded application that efficiently computes, visualizes and assesses significance of single- and paired-site CIFs and their evolutionary divergences for any RNA, protein, gene or genomic element sequence family. Multiple estimators of permutation P-values for CIF evolutionary divergences are provided along with confidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI.

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Lawrence, Travis J., Hadi-Nezhad, Fatemeh, Grosse, Ivo, Ardell, David H.. 2021-04-27. tSFM 1.0: tRNA Structure–Function Mapper. https://doi.org/10.1093/bioinformatics%2Fbtab247

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