[Genbank-bb] GenBank 192.0 : Problem with /anticodon ; correction regarding /frequency

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Wed Oct 24 15:27:38 EST 2012


Greetings GenBank Users,

Subsequent to the generation of the GenBank Release 192.0 data files,
it was discovered that the new "seq" field for the /anticodon qualifier
was improperly formatted:

a) The sequence of the anticodon was presented in the RNA alphabet
   rather than the DNA alphabet.

b) The sequence of the anticodon was presented in uppercase letters
   rather than lowercase letters.

Here is an example that illustrates these problems:

LOCUS       CP003206             2535346 bp    DNA     circular BCT 05-JUN-2012
DEFINITION  Corynebacterium diphtheriae 31A, complete genome.
ACCESSION   CP003206
VERSION     CP003206.1  GI:371577018
DBLINK      BioProject: PRJNA42399
....
     tRNA            complement(2017207..2017282)
                     /locus_tag="CD31A_t050"
                     /product="tRNA-Thr"
                     /anticodon=(pos:complement(2017247..2017249),aa:Thr,
                     seq:UGU)

The proper format for the qualifier is:

                     /anticodon=(pos:complement(2017247..2017249),aa:Thr,
                     seq:tgt)

Although it is too late to patch the files of Release 192.0, we have
deployed a new version of the flatfile generator into production that
fixes these formatting errors. Records appearing in the GenBank
Incremental Update (GIU) and RefSeq Incremental Update (RIU) products
at the NCBI FTP site utilize the correct format as of October 24 2012.
We expect that the same will be true for flatfiles viewed in
Entrez:Nucleotide within a week or so (the Entrez QA protocol requires
additional time).

Upon generation of December's GenBank Release 193.0, this error will
also be corrected in the release files.

Our apologies for any inconvenience that this causes for our users.

=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=

In Section 1.3 of the GenBank 192.0 Release Notes (gbrel.txt), we
incorrectly stated that:

  "So as of the October 2012 GenBank release, the /frequency qualifier has
been deprecated. Existing values for the qualifier are now presented via the
/note qualifier of source features, and GenBank submission tools are being
updated to cease support of /frequency."

However, this *only* applies to /frequency qualifiers on source
features.

Obviously, the /frequency qualifier provides information that is very
important for any variation feature, and it will continue to be supported
in that context. Only /frequency for source features has been deprecated.

Our apologies for mis-stating the nature of the /frequency change.

Mark Cavanaugh
GenBank
NCBI/NLM/NIH/HHS




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