Mapping transcriptome to genome

[Malovaan]

I'm wondering about the best way to determine the proportion of different transcriptome assemblies (assembled in trinity) which can be mapped to a reference genome assembly - basically for an indication of completeness.

I'm thinking that nucmer in the MUMer package might be a good place to start, with the transcripts as query and the genome as the reference sequence, but does anyone have a more cunning suggestion than that?

Thanks in advance!

[yzzhang]

the Sim4db http://www.ncbi.nlm.nih.gov/pubmed/21551146 and Exonerate https://www.ebi.ac.uk/~guy/exonerate/beginner.html work good