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GCG BLAST documentation: Question

Herve Recipon recipon at ncbi.nlm.nih.gov
Tue Aug 8 12:12:30 EST 1995


!>Hi,
!>
!>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
!>============================================================================



---

Sincerely,

--
Herve RECIPON, PhD.
 __  __  __  
/  \/  \/  \/1001001001     NCBI - NLM - NIH
\__/\__/\__/\               recipon at ncbi.nlm.nih.gov
                            1 / (301) 496-2475 ext 273
                            
========================================================================
For more details and advice on using BLAST programs send an e-mail to
blast at ncbi.nlm.nih.gov with "help" (without the quotes) in the body of 
the message to obtain the help file or read the BLAST Notebook, using a
WWW browser program to : http://www.ncbi.nlm.nih.gov/Recipon/index.html
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