GARAVELL@gunbrf.bitnet (02/07/91)
In article <9102061944.AA15931@genbank.bio.net> toms@fcs260c2.ncifcrf.gov (Tom Schneider) wrote: > GenBank already has the feature table, this would be completely sufficient to > satisfy everyone IF ONLY IT WERE KEPT UP TO DATE. There are already hundreds > of binding sites of various kinds, but only certain kinds are recorded in the > database. You don't need to go looking to create yet another feature of > GenBank, all you need to do is use what is there. > If you create consensus sequences you will be doing a huge disservice to > molecular biology by perpertrating this poor method. The PIR announced late last year that we were looking at making a PIR database for protein sequence features and motifs, and solicited comments. Tom, would you feel the same way about a protein database similar to the one Jamie Hayden says that GenBank is considering for nucleic acids? ------------------------------------------------------------------------ Dr. John S. Garavelli Database Coordinator Protein Identification Resource National Biomedical Research Foundation Washington, DC 20007 POSTMASTER@GUNBRF.BITNET
toms@fcs260c2.ncifcrf.gov (Tom Schneider) (02/08/91)
In article <9102062217.AA04849@genbank.bio.net> GARAVELL@gunbrf.bitnet writes: >In article <9102061944.AA15931@genbank.bio.net> >toms@fcs260c2.ncifcrf.gov (Tom Schneider) wrote: > >> GenBank already has the feature table, this would be completely sufficient to >> satisfy everyone IF ONLY IT WERE KEPT UP TO DATE. There are already hundreds >> of binding sites of various kinds, but only certain kinds are recorded in the >> database. You don't need to go looking to create yet another feature of >> GenBank, all you need to do is use what is there. >> If you create consensus sequences you will be doing a huge disservice to >> molecular biology by perpertrating this poor method. > >The PIR announced late last year that we were looking at making a PIR database >for protein sequence features and motifs, and solicited comments. Tom, would >you feel the same way about a protein database similar to the one Jamie Hayden >says that GenBank is considering for nucleic acids? John: Yes. It's the same principle. If a consensus is constructed, and made 'official' then better methods (ie, frequency matrix) will tend to be suppressed in people's minds. The dang consensus would have to be dropped eventually, since it isn't a good method, so why start now? This applies to any motif - DNA, RNA, protein - you can think of. This does NOT mean it isn't a good idea to make a carefully culled collection from which people could do anything they want. But that amounts to hard scientific work, with some judgement required. Also, to avoid data redundancy, you would want to do it by pointers to the database or by instructions for extracting the appropriate sequences (as in the Delila system). > Dr. John S. Garavelli > Database Coordinator > Protein Identification Resource > National Biomedical Research Foundation > Washington, DC 20007 > POSTMASTER@GUNBRF.BITNET Tom Schneider National Cancer Institute Laboratory of Mathematical Biology Frederick, Maryland 21702-1201 toms@ncifcrf.gov