-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear Ed,
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. 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. Cheers, Tim P.S.: if it were a silly question you would not have posed it, would you? ;-) On 06/23/2012 03:13 AM, Ed Pozharski wrote: > Silly question. > > Say I want to find every structure in the PDB with the exact > sequence or with perhaps 1-2 mutations. I know of two ways of > doing this. > > 1. Go to NCBI BLAST and run the sequence against the PDB subset. > The resulting list will have identities listed, so manual parsing > is doable if there aren't too many hits. > > 2. PDB and PDBe both have the search by sequence features. Trouble > is the default E value seems to be tailored to poor sequence > identity (which makes sense if you looking for potential MR > models). Sure, I can reduce the target E value, but it's a little > cumbersome and I have no idea what the target level should be so > that I don't get any 50% identical sequences yet not miss > single/double mutants. > > Wouldn't it be nice if one could use the sequence identity > cutoff/query coverage instead? Much more comprehensible than the > E-value. Is there a search engine that does that? Seems like a > fairly common need, and perhaps I just can't find on PDB website. > > Thanks in advance for any suggestions, > > Ed. > - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFP5R1ZUxlJ7aRr7hoRAmIXAJ47+STDlEmQ6iInnJPaiuL/aEIC3wCfbW1Y wxyvYSGRjXWwmQvqCnP4g3U= =WhkC -----END PGP SIGNATURE-----
