I would like to annotate all small RNAs in a genome based on different databases (e.g. miRBase) with the purpose of generating a gff file I can use for further analysis (and to practice).
I searched for tools to achieve this and my ideal tool has the following qualities: 1. I can provide various databases at the same time which are searched subsequently 2. A genome file not RNA-seq data is annotated.
Unfortunately all the tools I have found so far are not capable of doing so.
(This is what I found and why I don't ant to use it: Infernal is rather focused on structure based search and you can only use one DB for search, Unitas uses RNA-seq data as input, I do not get what database ShortStack is using)
Does anybody have recommendations which tool I can use? Also, if there are different possibilities of using databases for annotation I am happy for every hint ;)
This is rather new to me therefore, sorry if I missed a post already covering this or got something general wrong.