Custom anticodon models?

[austinv11]

Hello, is there any documentation available for creating custom tRNA models? Specifically, I am trying to annotate mitocondrial anticodons for many invertebrates and the -O option is unable to successfull annotate many of my tRNA sequences successfully

[patriciaplchan]

The tRNA models in tRNAscan-SE are covariance models utilizing Infernal for similarity search. For details of creating covariance models, please refer to the user guide of Infernal at http://eddylab.org/infernal/Userguide.pdf.