Question: What'S Faster? "Blastall -P Blastp" Or "Blastp?"
gravatar for Lee Katz
9.2 years ago by
Lee Katz3.0k
Atlanta, GA
Lee Katz3.0k wrote:

I am just wondering if anyone has done a timed test and/or a memory test with blastall compared to blastp. In other words, classic BLAST vs BLAST+. It'd be really interesting to get some kind of frequency distribution of the times it takes to blast one set of genes vs a database using each of the tools. The comparison could include any flavor of blast.

I know it's something I can do myself, but I'm being a little lazy about it and it could be something interesting that the biostar community can get together on.

frequency comparison blast • 3.7k views
ADD COMMENTlink modified 9.2 years ago by Simon Cockell7.3k • written 9.2 years ago by Lee Katz3.0k

I haven't done the formal test you're requesting, but I have seen a steady increase in performance with each new release. Unfortunately, I've also seen bugs in the newer releases too sometimes.

ADD REPLYlink written 9.2 years ago by Daniel Standage3.9k
gravatar for Simon Cockell
9.2 years ago by
Simon Cockell7.3k
Simon Cockell7.3k wrote:

This is pretty crude, but here we go. A very rapid comparison using nt and a 219 base query sequence:

$ time blastall -p blastn -i gene.fa -d /data/blastdb/nt -o out.blst  
32.19s user 3.01s system 99% cpu 35.469 total
$ time blastn -db /data/blastdb/nt -query gene.fa -out out.blstpl  
11.61s user 2.22s system 99% cpu 13.846 total

So, from this it looks like BLAST+ is somewhat faster, for a single sequence vs nt.

This is good, but I think we can do better. The BLAST+ paper reports significant speed-ups are possible when querying with long sequences. So, let's try a whole genome (even if it's only a bacterial one)...

$ time blastall -a 4 -p blastn -i NC_011353.fna -d /data/blastdb/nt -o out.blst  
46115.20s user 24.96s system 388% cpu 3:17:58.91 total
$ time blastn -num_threads 4 -db /data/blastdb/nt -query NC_011353.fna -out out.blstpl  
1462.23s user 7.98s system 233% cpu 10:29.37 total

This obviously isn't like-for-like with the first test, I ran these on 4 CPUs because I suspected they might take a while, and I was right. BLAST+ is offering a >30x speed up here. I would be interested to see if the reported reduction in memory usage is achieved too.

So it looks like for this test BLAST+ is faster (further scenarios are also offered in the paper linked above).

ADD COMMENTlink modified 7 months ago by RamRS26k • written 9.2 years ago by Simon Cockell7.3k
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