GCG BLAST documentation: Question

Dorothy Lowry lowry at russell.ucsf.edu.ucsf.edu
Mon Aug 7 19:05:40 EST 1995


I'm looking at page 6-7 of the GCG manual, and I'm trying to understand
what they are talking about regarding the bit score.  It says that for
a bit score of 30, one would have to have looked in a search space of
1 billion (or 2^30) to find this HSP by chance.

HOWEVER, in the next paragraph, we find that the search space size in
the example session is 235 x 12,496,420 x 0.13 or about 0.38 billion.

Then they say "therefore a bit score of 30 would not be significant".

What I do not understand, is that if we really had a search space of
0.38 billion bits, and we would need to have a search space of 1 billion
bits, before we would find that score by chance, then doesn't that mean
that a bit score of 30 WOULD be significant?  Because we didn't have to
search a search space 1 billion bits in size, before we found it?

Help - I'm confused!

-- Dorothy Lowry
Dorothy Lowry                                     email:  lowry at cgl.ucsf.edu
Sequence Analysis Service                         phone:  (415) 476-5379
Computer Graphics Lab UCSF                        fax:    (415) 582-1755
Box 0446 Room S926
513 Parnassus Avenue San Francisco, CA 94143-0446

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