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Old 09-27-2016, 09:12 AM   #1
fznajar
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Default command line BLASTN 2.3.0+ different hits from the web blastN

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?
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Old 09-27-2016, 09:17 AM   #2
GenoMax
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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.
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Old 09-27-2016, 09:30 AM   #3
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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?
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Old 09-27-2016, 11:37 AM   #4
GenoMax
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Two months is a long time so perhaps that is one factor for sure.
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Old 09-28-2016, 02:41 PM   #5
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Thanks GenoMax. Best
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Old 09-30-2016, 08:28 AM   #6
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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.
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