This is a simple and basic question but am so confused. I have generated my fasta sequence (from assembled transcript files and have used reference annotation file and fasta file for that) and now i want to perform blast2go on the generated fasta sequence . i want to run blast stand alone because blast2go is very slow and i have huge dataset, so i tried using the stand alone.
The first step is to craete a blastdb:
Which file should i use: a generated fasta file or the reference fasta file? Kindly help me , i want to blast my own set of generated sequences.
Any help will be appreciated.