I wonder if anyone else had this "problem" before or have any tips for me. If I blast against multiple databases I want to know where the hit is coming from. For example:
blastn -query fasta.fa -db "database1 database2" -outfmt 6
Probably I can determine the database based on the header of the hit, but would there be a better way? Can I also assume that the sequences from genbank always start with ">gi"?