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. 2019:1962:1-14.
doi: 10.1007/978-1-4939-9173-0_1.

tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences

Patricia P Chan  1 , Todd M Lowe  2
Affiliations

tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences

Patricia P Chan et al. Methods Mol Biol. 2019.

Abstract

Transfer RNAs are the largest, most complex non-coding RNA family, universal to all living organisms. tRNAscan-SE has been the de facto tool for predicting tRNA genes in whole genomes. The newly developed version 2.0 has incorporated advanced methodologies with improved probabilistic search software and a suite of new gene models, enabling better functional classification of predicted genes. This chapter describes the use of the UNIX command-driven and online web versions, illustrating different search modes and options.

Keywords: Covariance model; Gene prediction; Non-coding RNA; RNA secondary structure; Transfer RNA.

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Figures

Fig. 1
Fig. 1
Main search options for tRNAscan-SE online version. The minimum required options include the sequence source and the query sequence. BED file format can be optionally selected for output.
Fig. 2
Fig. 2
(A) Search mode and (B) extended options for tRNAscan-SE online version.
Fig. 3
Fig. 3
Search results of (A) predicted tRNA genes with scores, (B) secondary structure, (C) similar tRNA genes in GtRNAdb (2), and (D) scores of isotype-specific models for each predicted gene.
Fig. 4
Fig. 4
Additional search outputs include (A) linear secondary structures of predicted tRNA genes, (B) output BED file format if selected, and sequences in FASTA file.
See this image and copyright information in PMC

References

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