Tim,
> I did not understand your objection against solution 1 - is it because
> it is not automated? You can sort the results by max. Ident so that
> you can sroll down to the limit you set yourself.
More that it does not generate a list of PDB IDs. What I want to do is
to find every structure of a particular protein and line them all up. I
am not saying it's not doable with option 1, it's just not too convenient.
>
> Why do you think a identity cut-off was a good criterium? I usually
> cut by E-value because I assume the developers of blast know what they
> are doing and I have the impression they consider the E-value a better
> criterium than the max. Ident.
Because I want all the structures of a particular protein itself, not
it's homologues. I just went through several cycles of reducing E-value
down to 1e-100, and I still get one hit included at 88% identity.
Setting E-value cutoff to 0 doesn't work, it just returns them all.
Well, thanks to you I now see how to figure out the cutoff - the results
are sorted by E-values and list them, so I can just go to the first
non-identical hit and use a slightly smaller number. It's just that
sequence identity is easier for me to interpret and it's (emotionally)
easier to select a cutoff at, say, no more than 5 mutations rather than
E-value of 10e-150.
Cheers,
Ed.
Cheers
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
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