QN: Tell me about this GenBank search algorithm.

Keith Robison robison at nucleus.harvard.edu
Thu Apr 27 07:53:16 EST 1995

Hugh Evan Williams (hugh at goanna.cs.rmit.edu.au) wrote:
: 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).

FDF stands for Fast Data Finder, the marketing term for ABI's gizmo.
It is a chip originally developed by TRW for either the DOD or 
intelligence community (one can only imagine what sort of pattern
recognition those folks would be interested in :-)

: 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)?

You might try searching SeqAnalRef with FDF as a key, though I honestly
don't know how much is published.


If you want to make a rep for ABI or any of the other hardware-based 
supersearchers squirm, tell them you wish to use dystrophin as your 
protein query or the C.elegans contig as a nucleotide query.
-- many of these programs have hard-coded upper size limits on queries,
which are much smaller than the examples above.

Keith Robison
Harvard University
Department of Cellular and Developmental Biology
Department of Genetics / HHMI

robison at mito.harvard.edu 

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