I'm currently looking for sex-related genes and their pseudogenes in a reptilian that I sequenced, for which there is no reference.
I would like to look for specific gene names on my BLAST results which may subscribe to the description I made above.
My idea was to go through the literature which contains key words, such as "sex" "bird" "X" "y" "zw/zz" "reptiles", and extract words that are all in capitals, because that those might well be gene names, and then just get rid of common abbreviations.
Here's a side answer, that might help you drastically reduce your BLAST hits: as I read that you have a large bacterial contamination, I would BLAST with exclusion of all bacterial sequences. If you are using online's NCBI BLAST, you can exclude a complete taxonomic ID (Bacteria=2). If you want to reduce your BLAST hits, you can also consider BLASTing only a specific TaxID (this can be something as large as Sauropsida, for instance).