I am a bioinformatics novice, but I'm learning and managing. I've recently sequenced and am now analysing and annotating 8 transcriptomes from 2 different species. I've just recently ran a BLASTX against the the Drosophila melanogaster proteome (with .xml output).
The next thing I want to do is isolate all of the transcripts from that BLAST that did not hit anything in the Dmel proteome and BLAST them against the SwissProt Invertebrate database. As I said earlier, I am a novice, so please forgive me if this is a really simple thing to do. I would like to know, specifically, how I might approach subsetting the transcriptome fasta file to only contain the transcripts with no BLAST hits from Dmel.
Any and all insight is greatly appreciated.