ryals@KARYON.BIO.NET (Julie Ryals) (03/20/91)
GenBank Release 67 is Now Available
Release 67.0 is now available for use via the GenBank On-line Service
and is available for ftp from genbank.bio.net (134.172.1.160). Shipping
of magnetic tape subscriptions will begin by the end of this week.
The release notes accompanying release 67.0 include a description of
some proposed additions to the feature table. In an attempt to reach
all those affected by these changes, an excerpt from this section is
included below.
4.1.1. Feature Table Changes
The common GenBank/EMBL/DDBJ feature table format was finalized
more than two years ago and implemented in GenBank releases six months
ago. The feature table syntax was designed to be flexible, allowing the
addition of new feature keys and qualifiers to meet the changing needs of
the scientific community without disrupting existing software.
The staffs at GenBank, EMBL, and DDBJ have been collaborating on a number
of proposed additions to the feature table. We expect these changes to be
finalized in the very near future and to be implemented in GenBank
Release 68 (June 1991). The proposed additions are described briefly
below and will be documented fully in the Release Notes for Release 68.
If a more detailed description of the syntax is required earlier than
the next release, please send a request to genbank@genbank.bio.net, or
call (415) 962-7364.
We realize that we are proposing to make these additions with shorter
notice than is our usual policy, but feel that the demand for the
additional data is great enough to warrant proceeding at this time.
Our initial inquiries have indicated that these changes should not
present a problem for most users. The proposed additions do not alter
the structure of the feature table, but simply add new cases within the
existing format. Users may choose to ignore the new keys and qualifiers.
If these changes will have an adverse effect on your use of the database,
please contact us immediately at the address in the preceding paragraph
so we can consider adjusting our implementation schedule.
4.1.2. Proposed New Feature Keys
Key Description
--- -----------
primer Primer binding region used with PCR.
Note:
PCR components & reaction times can be stored under
the "/note=" qualifier. "primer" is distinguished
from "primer_bind" in that "primer" is used to denote
a PCR primer, and "primer_bind" is used for naturally
occurring primers.
STS Sequence Tagged Site. An operationally unique sequence
in the genome. This feature will identify the
combination of primer spans used in a PCR assay.
V_region
C_region
D_region
J_region
N_region
S_region These feature keys will be used to denote the spans
of immunological features
4.1.3. Proposed New Feature Qualifier
/map="text" map position of feature
4.1.4. Proposed Changes in Existing Qualifiers:
/codon_start= Indicates the first base of the first complete codon
in a CDS
Value format 1 or 2 or 3
Example /codon_start=2
Note: The original definition of this qualifier
was unclear, but with an intended meaining of
pointing to an absolute base position. This
created potential ambiguities for features that
spanned multiple entries.
/gene= Note: this qualifier may now be used with
all features
---------------
Julie Ryals
Assistant GenBank Manager
(415) 962-7309
ryals@genbank.bio.net