Path: utzoo!utgpu!watserv1!watmath!uunet!bionet!HISTONE.LANL.GOV!pgil
From: pgil@HISTONE.LANL.GOV (Paul Gilna)
Newsgroups: bionet.molbio.genbank
Subject: Re: Eukaryotic cis-acting transcription regulatory elements
Message-ID: <9102062259.AA01137@histone.lanl.gov>
Date: 6 Feb 91 22:59:50 GMT
Sender: daemon@genbank.bio.net
Lines: 56


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In article <9102051618.AA02080@replicon.lanl.gov> jeh@REPLICON.LANL.GOV
(Jamie Hayden) writes:
>
>GenBank's policy has been to not store consensus sequences, but rather
>the sequences from which such consensus sequences were derived.  Times
>change, however, and we are currently evaluating the idea of creating
>such a division within the database, a subsection of promotors and other
>important, conserved regions.

And Tom Schneider is quick to reply:


If you create consensus sequences you will be doing a huge disservice to
molecular biology by perpertrating this poor method.


	Tom, we would agree, at least in part. We have not consistently
	tracked such sequences in the past, indeed in part because of
	community responses similar in content to yours. It is not our
	intention at this point to place these sequences in the Flat
	File release of the database. Further, were this to be the
	case, we would give you and other members of the community
	ample opportunity to express their concern (or support). The
	primary purpose for these sequences is to aid us in our
	integrity checks placed upon incoming submitted data. We are
	currently completing software development on a module to check
	for the presence of vector sequence in submitted data.
	A preliminary version already in use has been enlightening!
	Such a module looks to a sub database of vector sequences
	to seek out similarities. One can quickly see that this method
	could be extended to other sub-databases, such as one
	containing consensus or signal sequences.

	So far, this has been discussed as an internal feature. I agree
	that the presence of such sequences in the public release
	database might add clutter to the conventional type of search.
	However, there is clearly a usefulness to the community in
	being able to search their own sequence data for specific signal
	sequences. *If* we place these data in the public domain, you
	may be assured that we will do so in a robust, parseable,
	unambiguous, clutter-free, and well-heralded manner.


Regards,

--paul

Paul Gilna
GenBank, Los Alamos