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 |
Download
Versioning
Add your version
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
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 IN pipelines
(136)[…] 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 […]
[…] 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 […]
[…] 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 […]
[…] 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. […]
[…] 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 reviews
Be the first to review tRNAscan-SE
