BLAST report interpretation.

Stefek Borkowski stefek at killspam.edu
Wed Dec 1 17:53:19 EST 2004

Hi again,
I would like to know what the BLAST interpretation really is in the case of 
comparing two sequences by the BLAST 2 Sequences online modul. The report 
goes as follows:
Identities = 32/114 (28%), Positives = 53/114 (46%), Gaps = 1/114 (0%)
I would say that the homology of the two proteins is equal to the value of 
"Identities", so it would be 28%. What about the "Positives" then? I happend 
somewhere in the literature on estimation of the homology between the 2 
proteins, stating that it is equal to 36%. This seems to be more or less the 
average arithmetic mean of "Identities" and "Positives", namely (28 + 46)/2 
is 37% which seems close to the literature value. Is my way of thinking 
correct or not necessarily. In other words, whot is the recommended 
algorithm of estimationg the homology of two sequences, on the basis of 
BLAST report.
Thanks for all your help. Kind regards,

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