BLAST best hit?

[mhadidi2002]

Hello,

I would like to ask about the standalone BLAST output best hit. Is it the first match for a given query sequence is always the best hit? As long as I know, it is sorted based on the E-value, the best match (with the lowest E-value) comes in the first, followed by the others. Right?

Best Regards,
BioinfGuy

[rhinoceros]

The lowest e-value doesn't necessarily always mean 'the best', but in most cases, yes. Even more so if you mask regions of low complexity..