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tRNAscan-SE: An improved tool for transfer RNA detection

Patricia Chan and Todd Lowe

School of Engineering, University of California, Santa Cruz, CA
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Current release: 1.3.1 (January 2012)

tRNAscan-SE was written in the PERL (version 5.0) 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 combines the specificity of the Cove/Infernal probabilistic 
RNA prediction package (1-2) with the speed and sensitivity of tRNAscan 1.3
(3) plus an implementation of an algorithm described by Pavesi and
colleagues (4), which searches for eukaryotic pol III tRNA promoters
(our implementation referred to as EufindtRNA). tRNAscan and
EufindtRNA are used as first-pass prefilters to identify "candidate"
tRNA regions of the sequence. These subsequences are then passed to
Cove for further analysis, and output if Cove confirms the initial
tRNA prediction. In this way, tRNAscan-SE attains the best of both
worlds: (1) a false positive rate equally low to using Cove analysis,
(2) the combined sensitivities of tRNAscan and EufindtRNA (detection
of 98-99% of true tRNAs), and (3) search speed 1,000 to 3,000 times
faster than Cove analysis and 30 to 90 times faster than the original
tRNAscan 1.3 (tRNAscan-SE uses both a code-optimized version of
tRNAscan 1.3 which gives a 300-fold increase in speed, and a fast C
implementation of the Pavesi et al. algorithm).

This distribution includes the PERL script tRNAscan-SE, all the files
necessary to compile and run the complete COVE package (version
2.4.4), all the files necessary to compile and run the modified
version of tRNAscan (version 1.4), and all the files needed to compile
and run eufindtRNA 1.0 (the cove programs, tRNAscan 1.4, and
eufindtRNA are included for use with the tRNAscan-SE program, but may
also be run as stand-alone programs).  Installation of the PERL
(Practical Extraction and Report Language, Larry Wall) interpreter
package version 5.0 or later is required to run the tRNAscan-SE PERL
script. An newer implementation of covariance model searches, Infernal, may
be used in place of Cove which allows for faster searches and new, specialized
search options. To use Infernal as the second-pass scanner or to include 
prediction of noncanonical introns and split fragments in archaeal tRNA 
genes, Infernal 1.0 must be pre-installed. Previous versions of Infernal
will not work with the covariance models provided with tRNAscan-SE. 
The Infernal source package can be downloaded at http://infernal.janelia.org/. 

For more detailed information, please read the following files:

  MANUAL       -- decription of program, run options & demo examples
                  (text) 
  Manual.ps    -- decription of program, run options & demo examples
                  (postscript format)
  INSTALL      -- instructions for installing the programs
  COPYING      -- copyright notice, and information on distribution policy
  FILES        -- overview of what the source files are
  GNULICENSE   -- Gnu Public License, version 2 (see COPYING)


You can obtain a copy of this software from
http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz
or
ftp://selab.janelia.org/pub/software/tRNAscan-SE.tar.Z

If you use this software, please cite the Nucleic Acids Research paper
describing the program & its analysis of several genomes (4).

If you have any questions, bug reports, or suggestions, please e-mail

   Todd Lowe
   lowe@soe.ucsc.edu

   Department of Biomolecular Engineering
   University of California
   1156 High Street
   Santa Cruz, ZA 95064


References

1. Eddy, S.R. and Durbin, R. (1994) "RNA sequence analysis using
   covariance models", Nucl. Acids Res., 22, 2079-2088.

2. Nawrocki, E.P., Kolbe, D.L. &  Eddy, S.R. (2010) "Infernal 1.0: 
   Inference of RNA Alignments", Bioinformatics, 25, 1335-1337.

3. Fichant, G.A. and Burks, C. (1991) "Identifying potential tRNA
   genes in genomic DNA sequences", J. Mol. Biol., 220, 659-671.

4. Pavesi, A., Conterio, F., Bolchi, A., Dieci, G., Ottonello,
   S. (1994) "Identification of new eukaryotic tRNA genes in genomic DNA
   databases by a multistep weight matrix analysis of transcriptional
   control regions", Nucl. Acids Res., 22, 1247-1256.

5. Lowe, T.M. & Eddy, S.R. (1997) "tRNAscan-SE: A program
   for improved detection of transfer RNA genes in genomic
   sequence", Nucl. Acids Res., 25, 955-964.
