Question: TBLASTN on a large DNA database (352GB)
0
gravatar for chippy8899
4.7 years ago by
chippy889910
chippy889910 wrote:

Hi,

I wonder if it possible to run command TBLASTN on a large metagenomic database(352G)? Wondering how long does it take if I m running on 4 cpus with memory available of 32G...

blast • 1.2k views
ADD COMMENTlink modified 4.7 years ago by Kamil2.0k • written 4.7 years ago by chippy889910

I am not 100% sure but based on my experience it might take 10-30 mins for one sequence.

ADD REPLYlink written 4.7 years ago by Sishuo Wang200
2
gravatar for Kamil
4.7 years ago by
Kamil2.0k
Baltimore
Kamil2.0k wrote:

USEARCH is "orders of magnitude faster than BLAST", so you might consider using that instead.

In a benchmark with 1,000 queries against a 15 Gb FASTA file containing 38.5 M proteins, USEARCH achieved a similar result to BLAST and finished in 9 minutes instead of 4.5 hours.

ADD COMMENTlink written 4.7 years ago by Kamil2.0k
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