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:
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$ which tRNAscan-SE
/local/cluster/tRNAscan-SE/bin/tRNAscan-SE
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help message:
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$ 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] <FASTA file(s)>
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 <model> : 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 <model> : 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 <file> : save final results in <file>
-f --struct <file> : save tRNA secondary structures to <file>
-s --isospecific <file> : save results using isotype-specific models in <file>
-m --stats <file> : save statistics summary for run in <file>
(speed, # tRNAs found in each part of search, etc)
-b --bed <file> : save results in BED file format of <file>
-j --gff <file> : save results in GFF3 file format of <file>
-a --fasta <file> : save predicted tRNA sequences in FASTA file format of <file>
-l --log <file> : save log of program progress in <file>
--detail : display prediction outputs in detailed view
--brief : brief output format (no column headers)
-? # : '#' in place of <file> chooses default name for output files
-p --prefix <label> : use <label> prefix for all default output file names
-d --progress : display program progress messages
-q --quiet : quiet mode (credits & run option selections suppressed)
-y --hitsrc : show origin of hits (Ts=tRNAscan 1.4, Eu=EufindtRNA,
Bo=Both Ts and Eu, Inf=Infernal)
Specify Alternate Cutoffs / Data Files:
-X --score <score> : set cutoff score (in bits) for reporting tRNAs (default=20)
-g --gencode <file> : use alternate genetic codes specified in <file> for
determining tRNA type
-z --pad <number> : use <number> nucleotides padding when passing first-pass
tRNA bounds predictions to CM analysis (default=8)
--len <length> : set max length of tRNA intron+variable region for legacy search mode
(default=116bp)
Misc Options:
-h --help : print this help message
-c --conf <file> : tRNAscan-SE configuration file (default: tRNAscan-SE.conf)
-Q --forceow : do not prompt user before overwriting pre-existing
result files (for batch processing)
--match <EXPR> : search only sequences with names matching <EXPR> string
(<EXPR> may contain * or ? wildcard chars)
--search <EXPR> : start search at sequence with name matching <EXPR> string
and continue to end of input sequence file(s)
Special Advanced Options (for testing & special purposes)
-U : search for tRNAs with alternate models defined in configuration file
-t --tscan : search using tRNAscan only (defaults to strict params)
--tmode <mode> : explicitly set tRNAscan params, where <mode>=R or S
(R=relaxed, S=strict tRNAscan v1.3 params)
-v --verbose <file> : save verbose tRNAscan 1.3 output to <file>
--nomerge : Keep redundant tRNAscan 1.3 hits (don't filter out multiple
predictions per tRNA identification)
-e --eufind : search using Eukaryotic tRNA finder (EufindtRNA) only
(defaults to Normal seach parameters when run alone,
or to Relaxed search params when run with Cove)
--emode <mode> : explicitly set EufindtRNA params, where <mode>=R, N, or S
(relaxed, normal, or strict)
--iscore <score> : manually set "intermediate" cutoff score for EufindtRNA
-r --fsres <file> : save first-pass scan results from EufindtRNA, tRNAscan, or
Infernal hmm in <file> in tabular results format
--mid : fast scan mode - search using Infernal with mid-level strictness of hmm filter
-F --falsepos <file> : save first-pass candidate tRNAs in <file> that were then
found to be false positives by second-pass analysis
--missed <file> : save all seqs that do NOT have at least one
tRNA prediction in them (aka "missed" seqs)
--thread <number> : number of threads used for running infernal (default is to use available threads)
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software ref: https://github.com/UCSC-LoweLab/tRNAscan-SE
research ref: https://doi.org/10.1093/nar/gkab688