tRNAscan-SE protocols

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

 (136)
2018
PMCID: 5805877
PMID: 29439039
DOI: 10.1128/genomeA.01395-17

[…] potential open reading frames (orfs) were identified with genemarks version 4.17 (6), and the functions of the orfs were predicted using blastp searches against the nonredundant ncbi database. trnascan-se version 1.3.1 (7) was employed to predict trnas., the ys35 genome comprises 93,296 bp of linear double-stranded dna with a g+c content of 49.3% and 13 trnas. in total, 172 orfs […]

2018
PMCID: 5855747
PMID: 29425128
DOI: 10.3390/ijms19020525

[…] manually adjusted following alignment to the related species, euonymus japonicas [58] to accurately determine the genes starting point, stop codons and exon borders. finally, blastn searches and trnascan-se v1.21 (university of california santa cruz, ca, usa) [60] were employed to verify both trna and rrna genes., a graphical cp genome map for c. edulis was completed using ogdraw […]

2018
PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] based on the local database with an e-value < 1e−6. then, the boundaries of each gene were confirmed by mitofy and exported as sequin formatted files. trna genes were further predicted by trnascan (http://lowelab.ucsc.edu/trnascan-se/)(supplementary table 43)., the paired-end reads for protocorm, juvenile tuber, immature tuber, mature tuber, scape samples were mapped to the g. elata […]

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

[…] with hsps, and in hsp regions (supplementary figs. 13, 14) were calculated from the results of blast searches against the busco ascomycota ‘ancestral’ database35., trna genes were predicted using trnascan-se41, 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. […]

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

[…] ascomycota ‘ancestral’ database35., trna genes were predicted using trnascan-se41, 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 our phylogenetic trees, trnas are identified with names such as s_cag1_ser1_babino_r2_i_25. the fields (separated […]

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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