tRNAscan-Se

Description

trnascan-se website

tRNA detection in large-scale genome sequences.

tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second. It was implemented for large-scale human genome sequence analysis, but is applicable to other DNAs as well. It applies our COVE software (see below) with a carefully built tRNA covariance model, while getting around COVE's speed limitations by using two tRNA finding programs from other research groups as fast first-pass scanners (Fichant and Burks', and an implementation of an algorithm from A. Pavesi's group). It runs on any UNIX system with Perl and a C compiler installed.

Environment Modules

Run module spider trnascan-se to find out what environment modules are available for this application.

Environment Variables

• HPC_TRNASCANSE_DIR - installation directory
• HPC_TRNASCANSE_BIN - executable directory
• HPC_TRNASCANSE_DOC - documentation directory

Citation

If you publish research that uses trnascan-se you have to cite it as follows:

Lowe, T. M., & Chan, P. P. (2016). tRNAscan-SE On-line: Search and Contextual Analysis of Transfer RNA Genes. Nucleic Acids Research, 44(W1), W54-W57. https://doi.org/10.1093/nar/gkw413

Chan, P. P., & Lowe, T. M. (2019). tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences. In M. Kollmar (Ed.), Gene Prediction: Methods and Protocols (pp. 1-14). Springer. https://doi.org/10.1007/978-1-4939-9173-0_1

Categories

biology, ngs