Seems like a solid option, seen it cited in coral miRNA paper, and listed in review paper Peterson et al. (2014) as one of the OG, more regularly maintained miRNA target prediction programs that takes user sequence input. Most recently updated 2010. Also, available as downloadable software run on linux/unix, so more reproducible than the other main miRNA target prediction softwares which are web based. Only problem is that the miRanda site (www.microrna.org) doesn’t seem to be functional… This is extra weird because the coral miRNA paper that used it was from 2022, which is quite recent.
miRanda tutorial
Found a site that appears to use the miRanda algorithm in a web based tool, and it seems to be functioning normally
I tried emailing the corresponding authors of the miRanda papers, but I’m not confident I’ll hear back. In the meantime I should also look into R package options, which weren’t really covered in the 2014 review I’ve been referencing.