nodalpoint.org - 10.000 times faster blast, in JAVA??? - Comments

BLAT and PatternHunter

maximilianh — Wed, 11 Oct 2006 11:27:17 -0400

thanks for the reference to PatternHunter... I've heard about it before but forgot it here.

Yes, it seems they simply put the database into memory. But well, given today's RAM prices that's not such a bad idea. BLAT does the same, with less sensitivity. And buying RAM is cheaper than buying some strange special hardware.

Neil: a) PatternHunter is also commercial though free for academic use.
b) You don't want to use BLAT in many appplications as it is a lot less sensitive than BLAST. I would rely on a blat only if the sequence is from the same or a very, very close species (like chimp or mouse to human) but that might also depend on the gene... So BLAT is really no alternative. Besides, BLAT is only free for academic use.

How can we know?

Neil — Wed, 11 Oct 2006 00:34:51 -0400

10 000 x does seem like an outrageous claim. How are we to know? The website is high on "corporate speak" and low on technical information. "More options than all other products combined", " a new paradigm in biotechnology", "the ultimate genomics search solution" etc. The only way to test their claims is to obtain the product. And that my friends is why open source is superior.
Itatsumaki has already noted the huge RAM dependency - 4 GB is hardly standard even on a modern laptop. If you want a fast, in-memory BLAST alternative, why not try BLAT?

RAM Dependent

Itatsumaki — Wed, 11 Oct 2006 00:03:26 -0400

I looked at this, and it seems like they're just playing tricks. Check out the RAM dependency they quote, it's huge. They suggest your required RAM is 24 times the size of the database in letters, divided by the word-size. So, for example if you try this algorithm against a large database like nt (non-redundant nucleotides) you would need a minimum of: 24 x 928,057,554 / 12 = 1.7 GB. So it seems like they are making a speed/space trade-off somewhere. Interestingly, that factor of 10k they quote sounds suspiciously like the difference between HD & memory access.

It also seems likely that the played around with the seeding. I think it's wrong to say that "local alignments have been worked on for decades without a lot of speed improvement". I think PatternHunter's asymmetric seeds are pretty convincing at doing just that, although I've never benchmarked it myself. Check out:
Bioinformatics. 2002 Mar;18(3):440-5.
PatternHunter: faster and more sensitive homology search.
Ma B, Tromp J, Li M.

10.000 times faster blast, in JAVA???

maximilianh — Fri, 29 Sep 2006 15:20:09 -0400

Given that the backbone of sequence analysis and as such bioinformatics is alignment, this news has the potential to shake some ground in the community: There is a new company claiming that their new BLAST is as sensitive but 10.000 times faster than the original by improving the seed searching phase. I'm very sceptical... local alignments have been worked on for decades without a lot of speed improvement while keeping accuracy. Which is why there are special hardware solutions for this problem (I wonder who is buying them).
But the company's website does not look like a joke and they're shipping demo versions... I have no clue how that could work. Suffix arrays? But that has been applied to local alignment seed search, right? Anyone out there with rumors about this company ?