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
