How to search for a ribozyme present on two RNA molecules at the same time? (enzyme strand on one RNA molecule and the substrate on another)
Is it possible to search for a particular ribozyme (consisting of a 'substrate' and 'enzyme' strand) present on two different RNA molecules? That is to say, search for a case where the substrate strand is present on one RNA molecule and the enzyme strand is present on a different RNA molecule.
I am looking at the following approaches:
- RNAMOT
- RNAMotif
- PatScan
- RNABOB
- BLAST
- BLAT
But reading the documentations of each, I absolutely cannot find anything on the matter I am investigating.
Is such a search at all possible? Are there any tools readily available to do this?
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