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Methods Mol Biol. 2019;1962:1-14. doi: 10.1007/978-1-4939-9173-0_1.

tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.

Author information

1
Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
2
Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA. tmjlowe@ucsc.edu.

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

PMID:
31020551
DOI:
10.1007/978-1-4939-9173-0_1
[Indexed for MEDLINE]

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