[BiO BB] genbank2swissprot ?

Dan Bolser dan.bolser at gmail.com
Wed Oct 10 05:26:07 EDT 2007

>From a recent 'refseq-announce' email;

*Announcing the availability of RefSeq-UniProtKB cross-link data*

In collaboration with UniProtKB  (http://www.pir.uniprot.org/) ,  the
RefSeqgroup is now  reporting explicit cross-references to Swiss-Prot
and  TrEMBL
proteins  that correspond to a RefSeq protein. These correspondences are
being calculated by the UniProtKB group, and will be updated every three
weeks to correspond to UniProt's release cycle. The data are being made
available from several sites within NCBI:

2.* **Links in NCBI's Protein database*

 Explicit links between corresponding RefSeq and Swiss-Prot proteins are now
provided within  the NCBI Protein database.  These links are available in
the 'Links' menu located at the upper right of the protein display page.
The link names are:

             * **Protein (RefSeq)*:          provides a link from a
Swiss-Prot record the corresponding RefSeq record
             * **Protein (UniProtKB*):       provides a link to the
equivalent Swiss-Prot record

4*. ftp sites*

A new file was added to the gene and refseq ftp sites to report the
relationship between NCBI Reference Sequence protein accessions and
UniProtKB protein accessions.  The new gene_refseq_uniprotkb_collab.gz file
specifies the corresponding pairs of NCBI and UniProtKB protein accessions.


The README file on the gene and refseq ftp sites has been updated to
document this addition. See:




On 09/10/2007, Dr. Christoph Gille <christoph.gille at charite.de> wrote:
> Many thanks Boris,
> this is quite good, though the table is incomplete.
> I think  I somewhere saw
> an assignment of mRNA to each  swissprot entry.
> Unfortunately I do not find it any more.
> Christoph
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