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 (numerous ``real'' tRNAs have been found just above the 20.0 cutoff). Knowledgable users may wish to experiment with this parameter to find unusual tRNAs or pseudogenes beyond the normal range of detection, keeping the preceding caveats in mind.
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.
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.
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.
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. In many mitochondrial and a number of
other microbial organisms, there are exceptions to this universal
translation code. This option allows the user to specify exceptions
to the universal code. Several alternate translation code files are
included in this package for convenience:
gcode.cilnuc for Ciliates, Dasycladacean, & Hexamita nuclear tRNAs gcode.echdmito for Echinoderm mitochondrial tRNAs gcode.invmito for Invertibrate mitochondrial tRNAs gcode.othmito for Mold, Protozoans, & Coelenterate mitochondrial tRNAs gcode.vertmito for Vertibrate mitochondrial tRNAs gcode.ystmito for Yeast mitochondrial tRNAs
The user may also create a new alternate translation file. An example of an alternate translation code specification file follows:
# Vertebrate mitochondrial translation codes # Format: <Codon> <3-letter AA abbreviation> <One letter AA abrev> TGA Trp W ATA Met M AGR Stp *
Comments or other information will be ignored on lines preceded by a
pound symbol '#'. Anticodon translation codes are specified by
placing the three base codon, the three letter amino acid
abbreviation, and the single letter amino acid abbreviation all on a
single line (each separated by a space or tab). Degenerate symbols
such as 'N', 'R', and 'Y' may also be used for codon specification.
Any codon not specified in the alternate genetic code file will use
the translation in the default 'universal' genetic code table that
occurs at the very end of the tRNAscan-SE.src source code file.
Changes can be made directly to the default translation table, but a
new 'make install' must be run to install the modified PERL script.
Note: this option does not have any effect when using the -T or
-E option (search using tRNAscan or EufindtRNA only) --- you must be
running in default or Cove only analysis mode.
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.