New global AllAllDB server at ETHZ

Sean Eddy sre at al.cam.ac.uk
Thu Aug 19 12:08:28 EST 1993


  > This new e-mail server selects matches from the all against all
  > database of SwissProt. This database contains all matches between all
  > sequence pairs of the SwissProt database with a similarity score of at
  > least 80 at optimal pam distance. Currently, there are about 1.7
  > million matches in the database. It can safely be said that any
  > relation between any two sequences in SwissProt which can be detected
  > by sequence alignment is recorded in this database.

Heh. A good way to touch off a discussion is to say that something's
"safely said" :)

Do you mean "which can be detected by *pairwise* sequence alignment"?
(I might even doubt that statement, depending on the scoring matrix
you use, and how stringent a score of "80" (bits?) is.)  Profile or
hidden Markov model alignments, using statistical descriptions of a
whole family, can potentially detect matches that pairwise alignments
would consider insignificant.  Are you arguing that anything a profile
or HMM can detect, there will be at least significant pairwise
alignment in your database? I'd be tempted to bet a few beers against
that proposition :)

--
- Sean Eddy
- Laboratory of Molecular Biology, MRC, Cambridge UK
- sre at mrc-lmb.cam.ac.uk




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