GO enrichment analysis for RNA-Seq data

[Tom2013]

I aim to compare transcriptomic response in a non-model species using RNA-Seq. So far, I have applied local blastx to analyzed all the expressed genes (around 60 000 genes) and obtained the xml file. I would like to conduct GO enrichment analysis. For GO enrichment analysis, I assume I need to do GO term mapping, annotation and then enrichment analysis according to Blast2Go pipeline. I planned to use Blast2Go, but it was too slow to my data set when I used it for mapping. Does anybody know which softwares I can use for the next analyses?

Thanks in advance.

[Mocca]

Check out Trinotate - took me a bit more than one week to do the annotation of my de novo transcriptome (some trial and error there). The blast part (only the mandatory one) took 4 days. I also tried the optional blast part (larger database) - that one I killed after 2 weeks as I didn't have more time availabe :-)