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. 2021 Oct 25;37(20):3654-3656.
doi: 10.1093/bioinformatics/btab247.

tSFM 1.0: tRNA Structure-Function Mapper

Travis J Lawrence  1   2 , Fatemeh Hadi-Nezhad  1 , Ivo Grosse  3   4 , David H Ardell  1   5
Affiliations

tSFM 1.0: tRNA Structure-Function Mapper

Travis J Lawrence et al. Bioinformatics. .

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.

Results: 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.

Availability and implementation: The data underlying this article are available on GitHub at https://github.com/tlawrence3/tSFM.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1.
Fig. 1.
Slopegraph of three different P-value estimate algorithms for KLD CIF divergences of L.enriettii clade tRNA genes (n = 160 genes) against human tRNA genes (n = 431 genes). PECDF′ is the naive Monte Carlo method with 10 000 permutations per feature, using pseudo-counts when there are fewer than S exceedances (by default, 10). PECDF terminates after S exceedances (PECDF) or a maximum of 10 000 permutations, using pseudo-counts unless there are S exceedances. PGPD uses algorithm Approximate with T = 500 target permutations and a maximum of 10 000 permutations. Colors show the harmonic mean of the number of sequences containing a given CIF in the two taxa. Points but not lines are jittered against overplotting. See online for color version.
See this image and copyright information in PMC

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