Search Mode Options

By default, the eukaryotic tRNA model is used for tRNA analysis. To select an alternate tRNA model for sequences from other sources (other phylogenetic domains or mitochondria/chloroplasts), use one of the following options:

-P

: search for prokaryotic tRNAs

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

: search for archaeal tRNAs

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

-O

: search for organellar (mitochondrial/chloroplast) tRNAs

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

: use general tRNA model

This option selects the original 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

: search using Cove analysis only

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

: show both primary & secondary structure score components to covariance model bit scores

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. It may be helpful to examine score breakdowns from known tRNAs in the organism of interest to get a frame of reference.

-D

: disable pseudogene checking

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.