Scott Coutts wrote:
>> You'd be better off finding both sequences (you can do this by simply
> using a keyword search) and then doing an alignment of the two
> sequences. You can do this on the web, using one of the 'clustal'
> programs, or you can download a stand-alone version of clustal and
> view your alignment using another downloadable program called
> 'genedoc'. I dont have the web addresses on hand at the moment, but
> you can easily find them with a google search.
>Thanks Scott for your quick answer. I just figured it out that I can use the
WWW module of BLAST called "BLAST 2 Sequences". Although I still have an
interpretation problem. Would you care to comment on the below, please.
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,
Stefek
