Path: utzoo!utgpu!watserv1!watmath!att!emory!wuarchive!bcm!bionet!kristoff From: kristoff@genbank.bio.net (David Kristofferson) Newsgroups: bionet.molbio.genbank Subject: Re: Eukaryotic cis-acting transcription regulatory elements Message-ID: Date: 7 Feb 91 00:08:06 GMT References: <9102062259.AA01137@histone.lanl.gov> Organization: GenBank Online Service Lines: 42 > 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. Paul, I would assume, however, that it would be easier to pull out vector sequences than consensus sequences as one often needs to use different searching methods for these latter purposes depending upon the extent of the ambiguity in the consensus sequence. I think that it might be dangerous for GenBank staff to try to make those kinds of assessments. Instead I would opt for leaving calls on consensus sequences to GenBank Curators who had specialized knowledge in the field. I would not even rely to a great extent on extracting such information from published literature since there is often considerable divergence of opinion here. Now to Tom, Ouch!! Are we bad or what 8-) 8-)?? The thing that I always find entertaining about this field is that when I was at the NCBI developers meeting last July, GenBank was being excoriated **for** including annotations for things like promoter sequences precisely for reasons along the lines I mentioned above. It did not appear then that NCBI intended to include this type of information in their up and coming GenInfo database, preferring instead a less elaborately annotated entry. However, the latest version I have heard indicated that their position was under revision due to input from yet other sections of the community. Never a dull moment, is there? 8-) In the absence of a concrete consensus, GenBank could spend a considerable amount of time doing and then undoing things. Dave