tSFM 1.0: tRNA Structure–Function Mapper

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

doi:10.1093/bioinformatics/btab247

Title: tSFM 1.0: tRNA Structure–Function Mapper

Journal Article · 26 April 2021 · Bioinformatics

DOI: https://doi.org/10.1093/bioinformatics/btab247 · OSTI ID:1827219

^[1]; Hadi-Nezhad, Fatemeh ^[2];

^[3]; Ardell, David H. ^[2]

Univ. of California, Merced, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Univ. of California, Merced, CA (United States)
Martin Luther University Halle (Germany); German Centre for Integrative Biodiversity Research (Germany)

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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Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1827219

Journal Information:: Bioinformatics, Journal Name: Bioinformatics Journal Issue: 20 Vol. 37; ISSN 1367-4803

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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