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tRNAscan-SE specifications

Information


Unique identifier OMICS_00385
Name tRNAscan-SE
Alternative names tRNAscan, tRNA Scan-SE
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Some DNA or RNA sequences.
Input format FASTA
Output data The default output for tRNAscan-SE includes the location of each identified tRNA, the predicted anticodon, introns (if present) and the tRNA covariance model score.
Operating system Unix/Linux
Computer skills Advanced
Version 1.21
Stability Stable
Maintained Yes

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Versioning


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Maintainer


  • person_outline Todd M. Lowe

Information


Unique identifier OMICS_00385
Name tRNAscan-SE
Alternative names tRNAscan, tRNA Scan-SE
Interface Web user interface
Restrictions to use None
Input data Some DNA or RNA sequences.
Input format FASTA
Output data The default output for tRNAscan-SE includes the location of each identified tRNA, the predicted anticodon, introns (if present) and the tRNA covariance model score.
Output format BED
Computer skills Basic
Version 2.0
Stability Stable
Source code URL http://trna.ucsc.edu/software/trnascan-se-2.0.0.tar.gz
Maintained Yes

Maintainer


  • person_outline Todd M. Lowe

Publications for tRNAscan-SE

tRNAscan-SE citations

 (2830)
library_books

The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites

2018
Sci Rep
PMCID: 5954100
PMID: 29765106
DOI: 10.1038/s41598-018-25981-w

[…] study, Klimov & OConnor provided an improved tRNA prediction in the house dust mite Dermatophagoides farinae including tRNAs of S. magnus for a comparison. Like Domes et al., Klimov and OConnor used tRNAscan-SE and ARWEN to predict tRNAs and infer their secondary structure. In contrast to Domes et al., the minimum free energy (MFE) of the constrained and unconstrained secondary structure was addi […]

library_books

Evolutionary instability of CUG Leu in the genetic code of budding yeasts

2018
Nat Commun
PMCID: 5951914
PMID: 29760453
DOI: 10.1038/s41467-018-04374-7

[…] s, in genes with HSPs, and in HSP regions (Supplementary Figs. , ) were calculated from the results of BLAST searches against the BUSCO Ascomycota ‘ancestral’ database.tRNA genes were predicted using tRNAscan-SE, with introns removed by our own Python code. In some Kluyveromyces species, the tLCAG gene was not predicted by tRNAscan-SE due to its unusually long intron but was found by BLASTN. In ou […]

call_split

Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes

2018
BMC Genomics
PMCID: 5946542
PMID: 29747572
DOI: 10.1186/s12864-018-4717-7
call_split See protocol

[…] d open-reading frames (ORF) were analyzed using program MEGA 5.0 []. The overlapping regions and intergenic spacers were counted manually []. The tRNA genes were identified using the software package tRNAscan-SE 2.0 (http://lowelab.ucsc.edu/tRNAscan-SE/) by eye, based on vertebrate mitochondrial anti-codon sequences and their secondary structure. In addition, the DOGMA annotation software was used […]

call_split

The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda)

2018
Sci Rep
PMCID: 5945635
PMID: 29749383
DOI: 10.1038/s41598-018-25759-0
call_split See protocol

[…] A and ORF finder (NCBI), and were confirmed by comparing nucleotide sequences with those from closely related nematodes. Putative secondary structures of 22 tRNA genes were inferred using the program tRNAscan-SE and verified by examining potential tRNA secondary structures and anticodon sequences. […]

library_books

Re exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences

2018
Sci Rep
PMCID: 5943242
PMID: 29743507
DOI: 10.1038/s41598-018-25585-4

[…] stop codons and intron–exon boundaries were manually annotated based on previously annotated information from the close relative A. thaliana. The complete structure of tRNA genes was validated using tRNAscan-SE v1.2.1. The systematic circular view of the chloroplast genome was created using OGDRAW and in-house customized perl script. Comparative syntenic maps were generated using circos following […]

call_split

Characterization and Genomic Study of Phage vB_EcoS B2 Infecting Multidrug Resistant Escherichia coli

2018
Front Microbiol
PMCID: 5945888
PMID: 29780362
DOI: 10.3389/fmicb.2018.00793
call_split See protocol

[…] tion annotation was performed using the BLAST tools at NCBI (http://blast.ncbi.nlm.nih.gov/Blast.cgi) against the non-redundant protein sequences database. Transfer RNAs (tRNAs) were identified using tRNAscan-SE (v1.23, http://lowelab.ucsc.edu/tRNAscan-SE) and ribosome RNAs (rRNAs) were determined using RNAmmer (v1.2, http://www.cbs.dtu.dk/services/RNAmmer/). DNAman was used to calculate molecular […]

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tRNAscan-SE institution(s)
Department of Biomolecular Engineering and the UCSC RNA Center, University of California Santa Cruz, Santa Cruz, CA, USA

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