------------------------------------------------------------- tRNAscan-SE: An improved tool for transfer RNA detection Patricia Chan and Todd Lowe School of Engineering, University of California, Santa Cruz, CA -------------------------------------------------------------- Current release: 1.3 (March 2011) 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.