When I annotate a transcriptome (or a set of transcripts), does it need to be annotated with, another transcriptome or do I need to use a genome? Should my blastdb be a genome, transcriptome, or protein data? My study species in a non-model organism (amphibian). Is it better to annotate with a closely related species of lower quality or a model organism of high quality? How do I determine quality from a database download? What database should I use, NCBI, Ensembl or UniProt?