QN: Tell me about this GenBank search algorithm.

Hugh Evan Williams hugh at goanna.cs.rmit.edu.au
Tue Apr 25 20:05:58 EST 1995


A friend posted me some mail recently concerning an ABI seminar he
attended in which they discussed (in true marketing jargon) a program
which claims to be able to search GenBank in 2 minutes with a "single
based FDF with 480 processors" (i get the impression this is some kind
virtual pipeline technology thing [though i'm not even sure what that is]
in which a computer has virtual processors, in a concept similar (?) to
virtual memory).

The program has three search methods: "FDF sliding window", "Smith-Waterman"
and FASTA. I am well versed in the latter two, but not in the first. Does
anyone know anything else about this FDF stuff? Does this software really
do a Smith-Waterman alignment on the whole of GenBank (seems doubtful)?

Any help would be greatly appreciated, as I seem to have run out of contacts
who can help...

Thanks in anticipation!

Hugh Williams.

--
| Hugh Williams (hugh at citri.edu.au) | "Any Warhol got it right, everybody gets |
| CITRI, 723 Swanston St, Carlton,  | the limelight. Andy Warhol got it wrong  |
| 3053, VIC  Australia.             | 15 minutes is too long" - TISM, 1995.    |





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