tRNAscan-SE specifications

Information


Unique identifier OMICS_00385
Name tRNAscan-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
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 <>

tRNAscan-SE articles

tRNAscan-SE citations

 (28)
2018
PMCID: 5805877

[…] 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: 5764944

[…] hits (e values, <10−10). we could also verify the absence of genes required for sulfate assimilation in s. fermentans. additionally, we identified 149 trna genes in the s. fermentans genome using trnascan-se (10)., this whole-genome shotgun project has been deposited in ddbj/ena/genbank under the accession no. jnfw00000000. the version described in this paper is the first version, […]

2017
PMCID: 5690336

[…] ncbi (https://blast.ncbi.nlm.nih.gov/blast.cgi) generated a further 373 hits. as was observed for s. fibuligera, also s. fodiens lacks genes required for sulfate uptake and assimilation (8). running trnascan on the scaffolds identified 162 trna genes (12)., this whole-genome shotgun project has been deposited in ddbj/ena/genbank under the accession no. jnfv00000000. the version described […]

2017
PMCID: 5522935

[…] functional gene annotation of the assembled genome was carried out by the rapid annotations using subsystems technology (rast) server (5). rrna and trna genes were determined by rnammer (6) and trnascan-se (7), respectively. the annotation predicted a total 9,248 coding sequences, 58 trna genes, and 3 rrna genes. the average nucleotide identity values of the genome by blastn (anib) […]

2016
PMCID: 5192330

[…] using blastp (e-value < 1e − 5) (table s1 in supplementary material available online at http://dx.doi.org/10.1155/2016/4512493). the rrna and trna genes were identified using rnammer [19] and trnascan [20], respectively. a comprehensive genome map containing coding and noncoding genes, cog annotations, and overall g+c content was plotted using perl-svg [21]., mummer is ideally suited […]

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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