blastx vs. blastn for metagenomics contigs

Question

[kelvinfrog75]

Hey, I got a question about using blast program for assembled contigs (in fasta format) of metagenomics samples. I saw many metagenomics papers from other groups used blastx to blast the contigs against reference protein database (which is virulence gene of bacteria). I just wonder what is the advantage of blastx over using blastn to blast the contigs against reference nucleotide? In my case, I saw there is a big difference between the results from blastx and blastn. I think my sample has a lot more hit when using blastx, so why blastx give me more hit than blastn?

Answer 1

[natasha.sernova]

See this post and suggestions there.

Why there is a big difference for blastn and blastx results of a given sequence

This post may also be useful:

A: Taxonomy Of Blast Hits