Program for clustering rna seq reads using protein database

[bohawk]

I have an RNA Seq data that I have used to assemble a de novo transcriptome, however, I am having trouble clustering it down into a final set of putative transcripts. I have used the Corset pipeline to cluster it down to 160,000 "genes" right now but beyond that I am stuck.

I have two unpublished protein databases for close relatives of my model and I was wondering if anyone had any suggestions for programs to map my putative transcripts to and cluster them even more?