tRNAscan-SE protocols

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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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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 in pipelines

 (706)
2018
PMCID: 5764924
PMID: 29326200
DOI: 10.1128/genomeA.01143-17

[…] prodigal version 1.20 (), genemarks version 4.08 (), and protein blast () and confirmed by the rapid annotations using subsystems technology (rast) version 2.0 server (). trnas were predicted using trnascan-se version 2.0 (), and the nucleotide homology of pvco-5 was determined using emboss stretcher ()., the genome of pvco-5 comprised double-stranded linear dna of 74,325 bp and a g+c content […]

2018
PMCID: 5764938
PMID: 29326214
DOI: 10.1128/genomeA.01422-17

[…] construction with pacbio rs ii and illumina hiseq dna to determine the complete genomic sequence of the b. melitensis qh61. the annotation was performed using genemarks (), repeat masker (), trf (), trnascan-se (), and rnammer ()., the whole-genome sequence of b. melitensis qh61 was found to be 3,311,767 bp in size and to be composed of two circular chromosomes, chromosome i (2,126,173 bp) […]

2018
PMCID: 5764942
PMID: 29326218
DOI: 10.1128/genomeA.01435-17

[…] assembled with a5-miseq software (). genome and subsystem-based annotations were performed by rapid annotation using subsystem technology (rast) (, ). trna gene detection was performed using the trnascan-se 2.0 tool (), whereas rrna genes were predicted using rnammer (). plasmid presence was checked by plasmidfinder software ()., after assembly, the two genomes were composed of 99 scaffolds. […]

2018
PMCID: 5773718
PMID: 29348333
DOI: 10.1128/genomeA.01418-17

[…] the previously known plasmid, pkap, of 41.7 kb (). the genome contains three rrna clusters in 16s-23s-5s configurations., gene annotation of the draft sequence was carried out using prodigal (), trnascan-se (), and rnammer () software tools. next to 36 trna genes, 1,080 protein coding sequences could be identified, of which, 787 could be functionally annotated by a similarity search […]

2018
PMCID: 5786510
PMID: 29403463
DOI: 10.3389/fmicb.2018.00011

[…] (altschul et al., ) and brig (alikhan et al., ). the presence of phages was screened using phaster (http://phaster.ca/) (arndt et al., ). trnas were screened using trna-se (http://lowelab.ucsc.edu/trnascan-se/) (lowe and chan, )., draft whole-genome sequence of strain sckp83 has been deposited into genbank under the accession number nokm00000000. short reads of the whole-genome sequence […]


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tRNAscan-SE in publications

 (2134)
PMCID: 5946542
PMID: 29747572
DOI: 10.1186/s12864-018-4717-7

[…] 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 […]

PMCID: 5945635
PMID: 29749383
DOI: 10.1038/s41598-018-25759-0

[…] 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., the datasets generated during and/or analysed during the current study are available […]

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 […]

PMCID: 5945888
PMID: 29780362
DOI: 10.3389/fmicb.2018.00793

[…] 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 […]

PMCID: 5935921
PMID: 29728068
DOI: 10.1186/s12864-018-4691-0

[…] with the protein function if it located in the same cluster as the annotated query sequence. gene ontologies (go) were annotated by blast2go software []. trna genes were identified with softwares trnascan-se [] and aragorn []., we defined genes with biased expression as either those homoeologous genes, with higher rpkm values two-fold or greater than the paired gene, as in previous studies […]


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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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