SEARCH RESULT FOR BLASTp from NCBI

[Keith Robison]

zainul at KB.USM.MY (Zainul Zain) writes:

>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
>sp|P13181|GAL2_YEAST   GALACTOSE TRANSPORTER (GALACTOSE P... 157    2.6e-25

>Could anybody tell me the significant of the two "High Score". I know 
>that the one with the smallest Poisson Probability is one to look at. 

>Actually, I have a lot to ask but let sort the above puzzle first. Thanks.

I would just point you to my little hypertext guide to sequence
searching (http://twod.med.harvard.edu/seqanal/), but I haven't added
the detailed explanation you are looking for!

BLAST produces ungapped local alignments.  If there is more than
one high-scoring region, BLAST will return each of them. Hence
the "High Score" column -- it is the score of the highest scoring
local alignment.  The Poisson score (sometimes) is calculated in
a way which counts all of the regions found.

Hope that helps...and I will update the guide.

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

krobison at nucleus.harvard.edu