fasta2gsi

detection of transfer RNA genes in genomic sequence

Install

All systems
curl cmd.cat/fasta2gsi.sh
Ubuntu
apt-get install trnascan-se
image/svg+xml Kali Linux
apt-get install trnascan-se
Windows (WSL2)
sudo apt-get update sudo apt-get install trnascan-se
Dockerfile
dockerfile.run/fasta2gsi

trnascan-se

detection of transfer RNA genes in genomic sequence

tRNAscan-SE identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at ~ 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.