Options for testing & special applications

-T

: search using tRNAscan only (defaults to strict search params)

Directs tRNAscan-SE to use only tRNAscan to analyze sequences. This mode will cause tRNAscan to default to using ``strict'' parameters (similar to tRNAscan version 1.3 operation). This mode of operation is slightly faster (about 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

: search using Eukaryotic tRNA finder (EufindtRNA) only

This option runs 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)

This option allows the user to explicitly set the parameters for EufindtRNA. 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 tRNAscan/EufindtRNA formatted output results in file

Saves 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

: search with Cove only those sequences & regions delimited in file (tabular results file format)

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. Also, if consecutive sequences have identical names in the sequence file being scanned, only the first sequence will be scanned in the regions defined in the -u file.

-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

: save all sequences without at least one tRNA hit in 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.