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Newsgroups: bit.listserv.info-gcg
Date:         Wed, 16 Dec 1992 00:05:39 -0600
Reply-To:     Maggie <smith@GCG.COM>
              <INFO-GCG@UTORONTO.BITNET>
From:         Maggie <smith@GCG.COM>
Subject:      RE: New Genbank (NCBI) database
Comments: To:

>Would GCG like to post on the INFO-GCG news-group/mailing-list
>instructions for changes that are required for setting up the new
>organisation of NCBI's Genbank 74.0 (released last with the 'organelle'
>division removed and a new 'est' division added).

>They may also like to comment on the extremely short notice that NCBI
>has given for these changes.  This strikes me as being rather
>insensitive to the needs of the database users and a poor start to their
>stewardship of this data.

>Gary Williams

>Computing Services Section,            Janet:       G.Williams@UK.AC.CRC
>MRC-CRC & Human Genome Mapping Centre, Internet:    G.Williams@CRC.AC.UK
>Watford Rd, HARROW, Middx, HA1 3UJ, UK
>Tel 081-869 3294   Fax 081-423 1275

Gary,

The modifications to accommodate the GenBank changes are attached below.
These changes are only necessary if the data is obtained directly from NCBI
for use with the GCG software.

We were aware of the new EST division and make note of how to accommodate it
in our 7.2 Release Notes.  Unfortunately, the removal of the Organelle
division caught us by surprise.  Since the posting of your message above, a
message has been posted on genbank-bb by David Lipman, of NCBI, apologizing
for the lack of advance notice and indicating that they will announce all
flatfile changes at least two releases (four months) in advance of a change.

Regards,

Maggie Smith
Genetics Computer Group

     ///////////////////-----------   -----------\\\\\\\\\\\\\\\\\\\\


Several files must be changed to accommodate the elimination of the
Organelle section of GenBank and to add the EST section.  All of these files
are in the directory GenRunData.

DBNAMES.MAP

    1) Edit the file dbnames.map to remove the line

         gborg          gb_or           or              ! genbank organelle

    2) Add the line (if it is not already present)

         gbest          gb_est          est             ! genbank est

GENDATA.FIL

    1) Edit the file gendata.fil to remove the line

         gb_or

    2) Add the line or remove the comment character (!) from the line
       if it is already present

         gb_est

GENEMBL.FARM

    1) Edit the file genembl.farm to remove the line

         gb_or

    2) Add the line or remove the comment character (!) from the line
       if it is already present

         gb_est

GENBANK.FARM

    1) Edit the file genbank.farm to remove the line

         gb_or

    2) Add the line or remove the comment character (!) from the line
       if it is already present

         gb_est

ORGANELLE.FARM

    1) Edit the file genbank.farm to remove the line

         gb_or

EST.FARM

    1) Create a file called EST.Farm.  It should contain the following:

         ..
         ! subsection for expressed sequence tag data

         gb_est


GCGUSERSPECS.COM

    1) Add the line (if it is not already present)

           $ Assign/NoLog "@genrundata:est.farm"              est



Michael Hogan
help@gcg.com
Newsgroups: bit.listserv.info-gcg