command line BLASTN 2.3.0+ different hits from the web blastN

[fznajar]

Hi,
I got different matches using the command line BLASTN 2.3.0+ (- remote) option from the NCBI website BlastN! Has anybody experienced this before?

[GenoMax]

There must be a difference in the command line you are using and the defaults on the web blast. Have you looked into that? Web blast is likely using 2.4.x, the latest. So if you want to really compare then upgrade your local blast to the latest as well.

[fznajar]

I did not. I found Blast 2.5.x. I will give this a shot. However, the difference in the matches is stark. Could the updates in the database itself make that much difference for ITS sequences in two months?

[GenoMax]

Two months is a long time so perhaps that is one factor for sure.

[fznajar]

Thanks GenoMax. Best

[maubp]

The NCBI BLAST website does a lot of parameter optimisation for you based things like query sequence length - the gap settings in particular are worth checking compared to the command line defaults.