Post-transcriptional Base Modifications

Energy parameter corrections for modified bases.

Many RNAs are known to be (heavily) modified post-trasnciptionaly. The best known examples are tRNAs and rRNAs. To-date, more than 150 different modifications are listed in the MODOMICS database (http://genesilico.pl/modomics/) [Boccaletto et al., 2022].

Many of the modified bases change the pairing behavior compared to their unmodified version, affecting not only the pairing partner preference, but also the resulting stability of the loops the base pairs may form.

Here, we provide a simple soft constraints callback implementation to correct for some well known modified bases where energy parameters are available for. This mechanism also supports arbitrary new modified base energy parameters supplied in JSON format (see Modified Bases for details).