How do I annotate a de novo assembled transcriptome against the GO database?

You can annotate the coding sequences in your transcripts using InterProScan. You can do this using WebServices or by downloading the tool and running it locally. Details can be found at: http://www.ebi.ac.uk/interpro/search/sequence-search/

This will predict GO terms based on domains detected using the mapping file here: http://geneontology.org/page/download-mappings

At this time this will give you a relatively high level set of GO annotations, but we are working with the Interpro group to incorporate Panther families and detailed GO annotations on Panther trees.

There are other tools that are not endorsed by GO, but may be of interest:

https://www.blast2go.com/ – but beware, many of the annotations propagated may be incorrect, depending in part on the phylogenetic distance to the nearest well-annotated genome

http://jamps.sourceforge.net/