Transcriptome BLASTing and finding miRNA targets

Question

[lindseytray]

Hello all,

I am trying to put together a project at a lab I am interning at where I want to search the transcriptomes of two symbionts (dinoflagellates and corals) to see if they have common miRNA targets. After isolating the RNA from both organisms and obtaining a the sequences, I was planning on blasting them together. Does anyone know how to blast transriptomes against each other or have any suggestions for me on what to do with the sequences when I get them back?

I'm just an undergrad trying to put together a molecular experiment with the resources available to me, so I am also open to other approaches to find gene-regulatory interactions between the two symbionts.

Thanks,

Lindsey