[BiO BB] GeneBank to SwissProt Mapping?

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Sat May 15 05:35:00 EDT 2004

Thanks Pamela for your suggestions, I have tried LocusLink (the 'loc2acc'
file) but I find many missing swissprot / trembl accession numbers. I
fear that the GO mapping could be incomplete for other resons too. 

Thanks Svensson for the offer of assistance below, but I am not sure how
having PID will help me. (sorry for my ignorance).

I know sptrembl has a good PIR mapping, can we get to PIR from GI?

I am running blast jobs at the minuite as the bind sequence file isn't too
big, but getting accurate 1-1 mapping means that I have to blast against
the full datasets and not some non redundant version thereof.

4 more days to go...

If anyone wants the data let me know.


On 14 May 2004, Svensson, B.A.T. (HKG) wrote:

>On Fri, 2004-05-14 at 15:28, Dan Bolser wrote:
>> On 14 May 2004, Svensson, B.A.T. (HKG) wrote:
>> >What data do you have to start with?
>> BIND.... I am thinking that blast will get the job done if I use refseq...
>I don't know about BIND, but if you have refseq, then you will be able
>to fetch the protein identifier (PID) as well as well as the official
>gene symbol from NCBI's data set UniGene (pre-blasted as to say), this
>should be enough to link to your data. If you need help with retrieving
>PID's and gene symbols, let me know and I can make a query in my own
>database to retrieve this data for you - or anything else you need from
>Precisely which EBI dataset would you like to link to?
>> >On Fri, 2004-05-14 at 15:10, Dan Bolser wrote:
>> >> Any body know how to map proteins from the NCBI to proteins from the EBI?
>> >> 
>> >> Cheers,
>> >> Dan.
>> >
>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org

More information about the BBB mailing list