Mike Cherry cherry at stout.Stanford.EDU
Mon Mar 28 11:10:06 EST 1994

In article <Pine.3.89.9403281600.A110-0100000 at>,
Zainul Zain <zainul at KB.USM.MY> wrote:
>Hello, My name is Nazar. I',m stuck with this problem of interpreting 
>the search result that was send back to me from NCBI.  Could anybody give 
>me some clue of what the "High Score" means etc.
>For Example:
>                                                                      Smallest
>                                                             High     Poisson 
>Sequences producing High-scoring Segment Pairs:              Score  Probability
>                                                                    P(N)
>sp|P11166|GTR1_HUMAN   GLUCOSE TRANSPOTER TYPE 1, ERYTHR...  2505   0.0

The High Score is simply the sum of all the values for the BLOSUM2
scoring matrix. The reference for the BLOSUM62 matrix is:

     Henikoff, Steven and Jorga G. Henikoff (1992).   Amino  acid
     substitution matrices from protein blocks. Proc. Natl. Acad.
     Sci. USA 89:10915-19.

For every amino acid aligned the value from the matrix is looked up
and added to the other values. So a higher score typically means a
better match. 

The Poisson probability is perhaps misleading in this case because the
first match is so good. The P(N) value of 0.0 is really a number less
than 1.0e-320. That means there is a less than 1 in 1.0e320 chance
that a match would be as good or better than the score of 2505 from a
search of the database involved above. The probability is based on the
Karlin and Altschul work.

     Karlin, Samuel and Stephen F. Altschul (1990).  Methods  for
     assessing the statistical significance of molecular sequence
     features by using general scoring schemes. Proc. Natl. Acad.
     Sci. USA 87:2264-68.

Some more information on the BLAST program and many references on
scoring matrix are available from the NCBI. Check out the information
returned from blast at when you send an e-mail with just
"help" as the body of the message.

J. Michael Cherry                       Internet: cherry at
Project Manager                         Saccharomyces Genome Database
Stanford DNA Sequence & Tech. Center    Department of Genetics
Stanford University School of Medicine  Stanford, CA 94305-5120

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