Entering edit mode
3.4 years ago
AfinaM
▴
30
Hi all,
I'm trying to set up a remote BLAST and based on the discussion in this post (Different results between remote and online blast) I then tried to use the search strategy file from the online BLAST to make sure that I can get the same result. Below is my command that I used:
blastn -remote -db nt -import_search_strategy strategy.asn -query test.fasta -max_target_seqs 10 -outfmt "6 sseqid sacc pident length evalue" -out blast.tsv
However, when I compared both result from remote and online BLAST, out of 10 hits, there will be 3 to 4 different hits and with different orders. Why is that?
Much appreciated on any advice to fix this. Thank you!
I don't find the reference to it for the moment but I seem to remember that it is not possible to mimic to online NCBI blast behaviour as it does things that us, normal mortals, are not allowed/able to do with the blast algorithm.
What you could do is to report this to the NBCI blast help desk and see what they say. (I would be interested in the feedback from them, so it would be appreciated if you come back to this post if you got any feedback from NCBI)