# tRNAscan SE 2.0.9 # tRNAscan-SE: An improved tool for transfer RNA detection tRNAscan-SE was written in the PERL (version 5) script language. Input consists of DNA or RNA sequences in FASTA format. tRNA predictions are output in standard tabular or ACeDB format. tRNAscan-SE does no tRNA detection itself, but instead combines the strengths of three independent tRNA prediction programs by negotiating the flow of information between them, performing a limited amount of post-processing, and outputting the results in one of several formats. tRNAscan-SE pioneers the large-scale use of covariance models to annotate tRNA genes in genomes. A covariance model is an implementation of a stochastic context-free grammar, able to integrate both primary sequence and secondary structure information, and is trained on an aligned, structurally annotated set of RNAs. Any given sequence can be searched for tRNAs by alignment to a tRNA covariance model. tRNAscan-SE 2.0 combines the use of the latest Infernal v1.1 (1) as the covariance model search engine and covariance models specifically trained and built using tRNA sequences from available genomes in the three domains of life for gene prediction. The method replaces the original use of COVE (2) with two prefilters - tRNAscan 1.3 (3) and an implementation of an algorithm described by Pavesi and colleagues (4) for searching eukaryotic pol III tRNA promoters (our implementation referred to as EufindtRNA), which is still available as a backward compatible option. Predicted tRNA genes will then be assessed using a set of isotype-specific covariance models. Comparative analysis among these models enables better annotation, particularly of atypical tRNAs, some of which may produce ÒrecodingÓ events due to mutations in the anticodon. The new tRNAscan-SE also enables better recognition of tRNA-derived SINEs that are abundant in many eukaryotic genomes by using a post quality filter. Location: ```console $ which tRNAscan-SE /local/cluster/tRNAscan-SE/bin/tRNAscan-SE ``` help message: ```console $ tRNAscan-SE --help tRNAscan-SE 2.0.9 (July 2021) Copyright (C) 2020 Patricia Chan and Todd Lowe University of California Santa Cruz Freely distributed under the GNU General Public License (GPLv3) Usage: tRNAscan-SE [-options] Scan a sequence file for tRNAs -- default: use Infernal & tRNA covariance models with eukaryotic sequences (use 'Search Mode Options' below to scan other types of sequences) Search Mode Options: -E : search for eukaryotic tRNAs (default) -B : search for bacterial tRNAs -A : search for archaeal tRNAs -M : search for mitochondrial tRNAs options: mammal, vert -O : search for other organellar tRNAs -G : use general tRNA model (cytoslic tRNAs from all 3 domains included) --mt : use mito tRNA models for cytosolic/mito detemination (if not specified, only cytosolic isotype-specific model scan will be performed) -I : search using Infernal default use with -E, -B, -A, or -G; optional for -O --max : maximum sensitivity mode - search using Infernal without hmm filter (very slow) -L : search using the legacy method (tRNAscan, EufindtRNA, and COVE) use with -E, -B, -A or -G -C --cove : search using COVE analysis only (legacy, extremely slow) default use with -O -H --breakdown : show breakdown of primary and secondary structure components to covariance model bit scores -D --nopseudo : disable pseudogene checking Output options: -o --output : save final results in -f --struct : save tRNA secondary structures to -s --isospecific : save results using isotype-specific models in -m --stats : save statistics summary for run in (speed, # tRNAs found in each part of search, etc) -b --bed : save results in BED file format of -j --gff : save results in GFF3 file format of -a --fasta : save predicted tRNA sequences in FASTA file format of -l --log : save log of program progress in --detail : display prediction outputs in detailed view --brief : brief output format (no column headers) -? # : '#' in place of chooses default name for output files -p --prefix