Blast: use best hit or top20 hits?

Question

[tianshenbio]

This question confused me a lot. I am blasting my transcriptome against NCBI nr database, then I will use blast2go for GO annotation. Should I only use the top hit or the top20 hits for it?

Someone told me I should use top20 since the top one is not necessarily the best to describe my query sequence. Another person suggested that I should only use the best hit since blasting more than 2 or 3 hits are random, and annotation is usually done with 1 best hit...

[h.mon]

Doesn't Blast2GO documentation give directions about best settings? If I am not mistaken, Blast2GO has an algorithm to weight multiple matches, such as matches with higher similarity / lower e-value have greater importance in deciding annotations - I would argue multiple hits are better than a single hit, then.

Anyway, I would think the default value is the recommended value. Isn't 20 the default Blast2GO value for number of hits?

[Gio12]

I agree with this. If I am correct, BLAST2GO has several filtering steps for blast hits (e.g. Blast Description Annotator (BDA)) that help you narrow down to the "best" hits.