Scott Coutts wrote:
>> ...
> Firstly, a technical point here... when your talking about genes, you
> should say 'similarity' rather than 'homology'. Either a gene is a
> homolog of another, or it's not.
>>http://homepage.usask.ca/~ctl271/857/def_homolog.shtml>http://www.biomedcentral.com/news/20040309/01>> But anyway...
>>>>> 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.
>> I'm not sure what figure they were quoting, but if it is properly
> quoted in the literature as a percentage, then it should include a
> statement of whether it is identities or similarities (positives),
> the region over which the count was obtained (if it's not mentioned
> the usually it's the whole protein).
>> You should read the documentation that comes with BLAST to understand
> how it works. The 'identities' is indicating the number of amino acids
> that are exactly the same, and the 'positives' is indicating the
> number that are similar (i.e. maintain similar properties, for
> example, both hydrophobic etc). You should also consider the E value
> that you're given.
Thank you so much Scott. Your explanation helped me a lot! I visited the
links you'd given me and already benefited from understanding this "E" value
calculated by BLAST. Though not everything is clear for me still, I have
made a big step forward. Thanks again. May you have a nice day :)
Special regards from Stefek
