Kristian G. AndersenGeverifieerd account

"BLAST documentation states "-max_target_seqs" parameter represents the "number of aligned sequences to keep". This statement is commonly inter- preted as meaning that BLAST will return the top N database hits for a sequence query if the value of max_target_seqs is set to N."

"BLAST returns the first N hits that exceed the specified E-value threshold, which may or may not be the highest scoring N hits. The invocation using the parameter "-max_target_seqs 1" simply returns the first good hit found in the database, not the best hit as one would assume."

"Worse yet, output produced depends on the order in which the sequences occur in the database. For the same query, different results will be returned by BLAST when using different versions of the database even if all versions contain the same best hit for this database sequence."

"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.