MOSAIK - parallel protein sequence guided assembly?

[liborm]

Hello,
we're going to sequence a transcriptome of eukaryote organism without a known genome. Now i'm thinking about the possibilities -- so two questions in one post:
Would it be possible to use protein sequences as a reference in MOSAIK?
and
What are the parallelization possibilities for using MOSAIK (for a cluster rather than SMP)?

Thanks