> Does anyone know of a program that will generate clover-leaf structures
> of tRNA genes from their coding sequence? I know of mfold, rnafold,
> loop-d-loop, and tRNA-Scan (the last one which nicely outputs the stems
> and loop regions from coding sequence), but none of these output the
> tRNA gene clover-leaf structure in standard, publishable orientation (at
> least not without much manipulation). Any/all suggestions appreciated.
how about using RnaViz?
It won't produce a standard clover-leaf layout by default but with a
suitable skeleton file it should do the job really well. Have a look: http://rrna.uia.ac.be/rnaviz/