tRNAscan-SE(1)              General Commands Manual             tRNAscan-SE(1)


              - a program for improved detection of transfer RNA genes in
              genomic sequence

       tRNAscan-SE [options] seqfile(s)

       tRNAscan-SE searches for transfer RNAs in genomic sequence seqfile(s)
       using three separate methods to achieve a combination of speed,
       sensitivity, and selectivity not available with each program

       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, ACeDB-compatible, or an
       extended format including tRNA secondary structure information.
       tRNAscan-SE does no tRNA detection itself, but instead combines the
       strengths of three independent tRNA prediction programs by negotiating
       the flow of information among them, performing a limited amount of
       post-processing, and outputting the result.

       tRNAscan-SE combines the specificity of the Cove probabilistic RNA
       prediction package (Eddy & Durbin, 1994) with the speed and sensitivity
       of tRNAscan 1.3 (Fichant & Burks, 1991) plus an implementation of an
       algorithm described by Pavesi and colleagues (1994) 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 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 650-fold increase in speed, and a
       fast C implementation of the Pavesi et al. algorithm).

       tRNAscan-SE was designed to make rapid, sensitive searches of genomic
       sequence feasible using the selectivity of the Cove analysis package.
       Search sensitivity was optimized with eukaryote cytoplasmic &
       eubacterial sequences, but it may be applied more broadly with a slight
       reduction in sensitivity.

       In the default tabular output format, each new tRNA in a sequence is
       consecutively numbered in the 'tRNA #' column.  'tRNA Bounds' specify
       the starting (5') and ending (3') nucleotide bounds for the tRNA.
       tRNAs found on the reverse (lower) strand are indicated by having the
       Begin (5') bound greater than the End (3') bound.

       The 'tRNA Type' is the predicted amino acid charged to the tRNA
       molecule based on the predicted anticodon (written 5'->3') displayed in
       the next column.   tRNAs that fit criteria for potential pseudogenes
       (poor primary or secondary structure), will be marked with "Pseudo" in
       the 'tRNA Type' column (pseudogene checking is further discussed in the
       Methods section of the program manual).  If there is a predicted intron
       in the tRNA, the next two columns indicate the nucleotide bounds.  If
       there is no predicted intron, both of these columns contain zero.

       The final column is the Cove score for the tRNA in bits of information.
       Specifically, it is a log-odds score: the log of the ratio of the
       probability of the sequence given the tRNA covariance model used
       (developed from hand-alignment of 1415 tRNAs), and the probability of
       the sequence given a simple random sequence model.  tRNAscan-SE counts
       any sequence that attains a score of 20.0 bits or larger as a tRNA
       (based on empirical studies conducted by Eddy & Durbin in ref #2).

       -h     Prints entire list of program options, each with a brief, one-
              line description.

       -P     This option selects the prokaryotic covariace model for tRNA
              analysis, and loosens the search parameters for EufindtRNA to
              improve detection of prokaryotic tRNAs.  Use of this mode with
              prokaryotic sequences will also improve bounds prediction of the
              3' end (the terminal CAA triplet).

       -A     This option selects an archaeal-specific covariance model for
              tRNA analysis, as well as slightly loosening the EufindtRNA
              search cutoffs.

       -O     This parameter bypasses the fast first-pass scanners that are
              poor at detecting organellar tRNAs and runs Cove analysis only.
              Since true organellar tRNAs have been found to have Cove scores
              between 15 and 20 bits, the search cutoff is lowered from 20 to
              15 bits.  Also, pseudogene checking is disabled since it is only
              applicable to eukaryotic cytoplasmic tRNA pseudogenes.  Since
              Cove-only mode is used, searches will be very slow (see -C
              option below) relative to the default mode.

       -G     This option selects the general tRNA covariance model that was
              trained on tRNAs from all three phylogenetic domains (archaea,
              bacteria, & eukarya).  This mode can be used when analyzing a
              mixed collection of sequences from more than one phylogenetic
              domain, with only slight loss of sensitivity and selectivity.
              The original publication describing this program and tRNAscan-SE
              version 1.0 used this general tRNA model exclusively.  If you
              wish to compare scores to those found in the paper or scans
              using v1.0, use this option.  Use of this option is compatible
              with all other search mode options described in this section.

       -C     Directs tRNAscan-SE to analyze sequences using Cove analysis
              only.  This option allows a slightly more sensitive search than
              the default tRNAscan + EufindtRNA -> Cove mode, but is much
              slower (by approx. 250 to 3,000 fold).  Output format and other
              program defaults are otherwise identical to the normal analysis.

       -H     This option displays the breakdown of the two components of the
              covariance model bit score.  Since tRNA pseudogenes often have
              one very low component (good secondary structure but poor
              primary sequence similarity to the tRNA model, or vice versa),
              this information may be useful in deciding whether a low-scoring
              tRNA is likely to be a pseudogene.  The heuristic pseudogene
              detection filter uses this information to flag possible
              pseudogenes -- use this option to see why a hit is marked as a
              possible pseudogene.  The user may wish to examine score
              breakdowns from known tRNAs in the organism of interest to get a
              frame of reference.

       -D     Manually disable checking tRNAs for poor primary or secondary
              structure scores often indicative of eukaryotic pseudogenes.
              This will slightly speed the program & may be necessary for non-
              eukaryotic sequences that are flagged as possible pseudogenes
              but are known to be functional tRNAs.

       -o <file>
              Output final results to <file>.

       -f <file>
              Save final results and Cove tRNA secondary structure predictions
              to <file>.  This output format makes visual inspection of
              individual tRNA predictions easier since the tRNA sequence is
              displayed along with the predicted tRNA base pairings.

       -a     Output final results in ACeDB format instead of the default
              tabular format.

       -m <file>
              Save statistics summary for run.  This option directs tRNAscan-
              SE to write a brief summary to <file> which contains the run
              options selected as well as statistics on the number of tRNAs
              detected at each phase of the search, search speed, and other
              bits of information.  See Manual documentation for explanation
              of each statistic.

       -d     Display program progress.  Messages indicating which phase of
              the tRNA search are printed to standard output. If final results
              are also being sent to standard output, some of these messages
              will be suppressed so as to not interrupt display of the

       -l <file>
              Save log of program progress in <file>.  Identical to -d option,
              but sends message to <file> instead of standard output.  Note:
              the -d option overrides the -l option if both are specified on
              the same command line.

       -q     Quiet mode: the credits & run option selections normally printed
              to standard error at the beginning of each run are suppressed.

       -b     Use brief output format.  This eliminates column headers that
              appear by default when writing results in tabular output format.
              Useful if results are to be parsed or piped to another program.

       -N     This option causes tRNAscan-SE to output a tRNA's corresponding
              codon in place of its anticodon.

              The '#' symbol may be used as shorthand to specify "default"
              file names for output files.  The default file names are
              constructed by using the input sequence file name, followed by
              an extension specifying the output file type <seqfile.ext> where
              '.ext' is:

              Extension   Option    Description
              ---------   ------    -----------
               .out        -o       final results
               .stats      -m       summary statistics file
               .log        -l       run progress file
               .ss         -f       secondary structures save file
               .fpass.out  -r       formatted, tabular output
                                    from first-pass scans
               .fpos       -F       FASTA file of tRNAs identified in
                             first-pass scans that were found to be
                             false positives by Cove analysis


              1) If the input sequence file name has the extensions '.fa' or
              '.seq', these extensions will be removed before using the
              filename as a prefix for default file names.  (example -- input
              file name Mygene.seq will have the output file name Mygene.out
              if the '-o#' option is used).

              2) If more than one sequence file is specified on the command
              line, the "default" output file prefix will be the name of the
              FIRST sequence file on the command line.  Use the -p option to
              change this default name to something more appropriate when
              using more than one sequence file on the command line.

       -p <label>
              Use <label> prefix as the default output file prefix when using
              '#' for file name specification.  <label> is used in place of
              the input sequence file name.

       -y     This option displays which of the first-pass scanners detected
              the tRNA being output.  "Ts", "Eu", or "Bo" will appear in the
              last column of Tabular output, indicating that either tRNAscan
              1.4, EufindtRNA, or both scanners detected the tRNA,

       -X <score>
              Set Cove cutoff score for reporting tRNAs (default=20).  This
              option allows the user to specify a different Cove score
              threshold for reporting tRNAs.  It is not recommended that
              novice users change this cutoff, as a lower cutoff score will
              increase the number of pseudogenes and other false positives
              found by tRNAscan-SE (especially when used with the "Cove only"
              scan mode).  Conversely, a higher cutoff than 20.0 bits will
              likely cause true tRNAs to be missed by tRNAscan (numerous
              "real" tRNAs have been found just above the 20.0 cutoff).
              Knowledgable users may wish to experiment with this parameter to
              find very unusual tRNAs or pseudogenes beyond the normal range
              of detection with the preceding caveats in mind.

       -L <length>
              Set max length of tRNA intron+variable region (default=116bp).
              The default maximum tRNA length for tRNAscan-SE is 192 bp, but
              this limit can be increased with this option to allow searches
              with no practical limit on tRNA length.  In the first phase of
              tRNAscan-SE, EufindtRNA searches for A and B boxes of <length>
              maximum distance apart, and passes only the 5' and 3' tRNA ends
              to covariance model analysis for confirmation (removing the bulk
              of long intervening sequences).  tRNAs containing group I and II
              introns have been detected by setting this parameter to over 800
              bp.  Caution: group I or II introns in tRNAs tend to occur in
              positions other than the canonical position of protein-spliced
              introns, so tRNAscan-SE mispredicts the intron bounds and
              anticodon sequence for these cases.  tRNA bound predictions,
              however, have been found to be reliable in these same tRNAs.

       -I <score>
              This score cutoff affects the sensitivity of the first-pass
              scanner EufindtRNA.  This parameter should not need to be
              adjusted from its default values (variable depending on search
              mode), but is included for users who are familiar with the
              Pavesi et al. (1994) paper and wish to set it manually.  See
              Lowe & Eddy (1997) for details on parameter values used by
              tRNAscan-SE depending on the search mode.

       -B <number>
              By default, tRNAscan-SE adds 7 nucleotides to both ends of tRNA
              predictions when first-pass tRNA predictions are passed to
              covariance model (CM) analysis.  CM analysis generally trims
              these bounds back down, but on occassion, allows prediction of
              an otherwise truncated first-pass tRNA prediction.

       -g <file>
              Use exceptions to "universal" genetic code specified in <file>.
              By default, tRNAscan-SE uses a standard universal codon -> amino
              acid translation table that is specified at the end of the
              tRNAscan-SE.src source file.  This option allows the user to
              specify exceptions to the default translation table.  The user
              may use any one of several alternate translation code files
              included in this package (see files documentation for
              specification of file format, or refer to included examples

              Note: this option does not have any effect when using the -T or
              -E options -- you must be running in default or Cove only
              analysis mode.

       -c <file>
              For users who have developed their own tRNA covariance models
              using the Cove program "coveb" (see Cove documentation), this
              parameter allows substitution for the default tRNA covariance
              models.  May be useful for extending Cove-only mode detection of
              particularly strange tRNA species such as mitochondrial tRNAs.

       -Q     By default, if an output result file to be written to already
              exists, the user is prompted whether the file should be over-
              written or appended to.  Using this options forces overwriting
              of pre-existing files without an interactive prompt.  This
              option may be handy for batch-processing and running tRNAscan-SE
              in the background.

       -n <EXPR>
              Search only sequences with names matching <EXPR> string.  <EXPR>
              may contain * or ? wildcard characters, but the user should
              remember to enclose these expressions in single quotes to avoid
              shell expansion.  Only those sequences with names (first non-
              white space word after ">" symbol on FASTA name/description
              line) matching <EXPR> are analyzed for tRNAs.

       -s <EXPR>
              Start search at first sequence with name matching <EXPR> string
              and continue to end of input sequence file(s).  This may be
              useful for re-starting crashed/aborted runs at the point where
              the previous run stopped.  (If same names for output file(s) are
              used, program will ask if files should be over-written or
              appended to -- choose append and run will successfully be
              restarted where it left off).

       -T     Directs tRNAscan-SE to use only tRNAscan to analyze sequences.
              This mode will default to using "strict" parameters with
              tRNAscan analysis (similar to tRNAscan version 1.3 operation).
              This mode of operation is faster (3-5 times faster than default
              mode analysis), but will result in approximately 0.2 to 0.6
              false positive tRNAs per Mbp, decreased sensitivity, and less
              reliable prediction of anticodons, tRNA isotype, and introns.

       -t <mode>
              Explicitly set tRNAscan params, where <mode> = R or S
              (R=relaxed, S=strict tRNAscan v1.3 params).  This option allows
              selection of strict or relaxed search parameters for tRNAscan
              analysis.  By default, "strict" parameters are used.  Relaxed
              parameters may give very slightly increased search sensitivity,
              but increase search time by 20-40 fold.

       -E     Run EufindtRNA alone to search for tRNAs.  Since Cove is not
              being used as a secondary filter to remove false positives, this
              run mode defaults to "Normal" parameters which more closely
              approximates the sensitivity and selectivity of the original
              algorithm describe by Pavesi and colleagues (see the next
              option, -e for a description of the various run modes).

       -e <mode>
              Explicitly set EufindtRNA params, where <mode>= R, N, or S
              (relaxed, normal, or strict).  The "relaxed" mode is used for
              EufindtRNA when using tRNAscan-SE in default mode.  With relaxed
              parameters, tRNAs that lack pol III poly-T terminators are not
              penalized, increasing search sensitivity, but decreasing
              selectivity.  When Cove analysis is being used as a secondary
              filter for false positives (as in tRNAscan-SE's default mode),
              overall selectivity is not decreased.

              Using "normal" parameters with EufindtRNA does incorporate a log
              odds score for the distance between the B box and the first
              poly-T terminator, but does not disqualify tRNAs that do not
              have a terminator signal within 60 nucleotides.  This mode is
              used by default when Cove analysis is not being used as a
              secondary false positive filter.

              Using "strict" parameters with EufindtRNA also incorporates a
              log odds score for the distance between the B box and the first
              poly-T terminator, but _rejects_ tRNAs that do not have such a
              signal within 60 nucleotides of the end of the B box.  This mode
              most closely approximates the originally published search
              algorithm (3); sensitivity is reduced relative to using
              "relaxed" and "normal" modes, but selectivity is increased which
              is important if no secondary filter, such as Cove analysis, is
              being used to remove false positives.  This mode will miss most
              prokaryotic tRNAs since the poly-T terminator signal is a
              feature specific to eukaryotic tRNAs genes (always use "relaxed"
              mode for scanning prokaryotic sequences for tRNAs).

       -r <file>
              Save tabular, formatted output results from tRNAscan and/or
              EufindtRNA first pass scans in <file>.  The format is similar to
              the final tabular output format, except no Cove score is
              available at this point in the search (if EufindtRNA has
              detected the tRNA, the negative log likelihood score is given).
              Also, the sequence ID number and source sequence length appear
              in the columns where intron bounds are shown in final output.
              This option may be useful for examining false positive tRNAs
              predicted by first-pass scans that have been filtered out by
              Cove analysis.

       -u <file>
              This option allows the user to re-generate results from regions
              identified to have tRNAs by a previous tRNAscan-SE run.  Either
              a regular tabular result file, or output saved with the -r
              option may be used as the specified <file>.  This option is
              particularly useful for generating either secondary structure
              output (-f option) or ACeDB output (-a option) without having to
              re-scan entire sequences.  Alternatively, if the -r option is
              used to generate the previous results file, tRNAscan-SE will
              pick up at the stage of Cove-confirmation of tRNAs and output
              final tRNA predicitons as with a normal run.

              Note: the -n and -s options will not work in conjunction with
              this option.

       -F <file>
              Save first-pass candidate tRNAs in <file> that were then found
              to be false positives by Cove analysis.  This option saves
              candidate tRNAs found by either tRNAscan and/or EufindtRNA that
              were then rejected by Cove analysis as being false positives.
              tRNAs are saved in the FASTA sequence format.

       -M <file>
              This option may be used when scanning a collection of known tRNA
              sequences to identify possible false negatives (incorreclty
              missed by tRNAscan-SE) or sequences incorrectly annotated as
              tRNAs (correctly passed over by tRNAscan-SE).  Examination of
              primary & secondary structure covariance model scores (-H
              option), and visual inspection of secondary structures (use -F
              option) may be helpful resolving identification conflicts.

       User Manual and tutorial: (postscript), MANUAL (text)

       No major bugs known.

       This software and documentation is Copyright (C) 1996, Todd M.J. Lowe &
       Sean R. Eddy.  It is freely distributable under terms of the GNU
       General Public License. See COPYING, in the source code distribution,
       for more details, or contact me.

       Todd Lowe
       Dept. of Genetics, Washington Univ. School of Medicine
       660 S. Euclid Box 8232
       St Louis, MO 63110 USA
       Phone: 1-314-362-7667
       FAX  : 1-314-362-2985

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

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

       3. 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.

       4. 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.

tRNAscan-SE 1.1                  November 1997                  tRNAscan-SE(1)