Travis J Lawrence1,2, Fatemeh Hadi-Nezhad1, Ivo Grosse3,4, David H Ardell1,5. 1. Quantitative and Systems Biology Program, University of California, Merced, United States of America. 2. Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee, 37830, United States of America. 3. Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany. 4. German Center of Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany. 5. Department of Molecular and Cell Biology, University of California, Merced, California 95343, United States of America.
Abstract
MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: 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 condidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.
MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: 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 condidence intervals. tSFM is implemented in Python 3 with compiled C extensions and is freely available through GitHub (https://github.com/tlawrence3/tSFM) and PyPI. SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.
Authors: Paul Kelly; Fatemeh Hadi-Nezhad; Dennis Y Liu; Travis J Lawrence; Roger G Linington; Michael Ibba; David H Ardell Journal: PLoS Negl Trop Dis Date: 2020-02-27