tRNAscan-SE statistics
Citations per year
Tool usage distribution map
Associated diseases
Popular tool citations
Related tools
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 |
Download
Versioning
No version available
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 2.0: Improved Detection and Functional Classification of Transfer RNA Genes.
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs.
TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
tRNAscan-SE citations
(2830)The mitochondrial genome of the oribatid mite Paraleius leontonychus: new insights into tRNA evolution and phylogenetic relationships in acariform mites
[…] 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 […]
Evolutionary instability of CUG Leu in the genetic code of budding yeasts
[…] 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 […]
Multiple independent structural dynamic events in the evolution of snake mitochondrial genomes
[…] 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 […]
The bipartite mitochondrial genome of Ruizia karukerae (Rhigonematomorpha, Nematoda)
[…] 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. […]
Re exploration of U’s Triangle Brassica Species Based on Chloroplast Genomes and 45S nrDNA Sequences
[…] 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 […]
Characterization and Genomic Study of Phage vB_EcoS B2 Infecting Multidrug Resistant Escherichia coli
[…] 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 […]
tRNAscan-SE reviews
Be the first to review tRNAscan-SE