Im a masters student trying my hand at de-novo assembly (eukaryotic, multicellular algae). I followed the basic FastQC, Prinseq, Adaptor trimming steps and plan to to run SGA next. I might run the sequences through another assembler later on, but can someone tell me what else could I do with my sequences?

I'm interested in certain genes and wanted to compare these genes in another organism, can someone describe what sort of comparitive tools can I use? Becuase I haven't actually done any experiments to see Expression of these genes, is it still possible to annotate my genome and still have a part of my project be about comparing it with another organism?