Kristian G. AndersenGeverifieerd account

"Even ordering the database in a different way would cause BLAST to return a different "top hit" when setting the max_target_seqs parameter to 1."

"...the incorrect use of the max_target_seqs parameter can result in invalid ana- lytic results. A biodefense screening tool might miss the presence of Bacillus anthracis simply because a Bacillus cereus sequence occurs before B. anthracis in the data- base."

I see this *much* more as an issue with Blast than the users. It’s interpreted that way, because that’s the way it makes the most sense.

True but people use this option to speed up BLAST which makes no sense if all it does is to report fewer results.

I think there are a number of reasons why people chose this option, speed, as you say, being one of them. But the issue is that people might not realize that when they gain speed, they lose depth - especially since the online version of blast behaves differently.

'People', of course, being non-programmers. Programmers are not really people in the strictest sense. More like Gods.

I use the option to reduce the size of the output file.

Aren’t num_descriptions & num_alignments for that?