[BiO BB] GeneBank to SwissProt Mapping?

[Dan Bolser]

On Sat, 15 May 2004, Anand Kumar wrote:

>Dan,
>
>> 
>> To clarify what I am doing: 
>> 
>> I take BIND protein interaction data, and for each sequence available in
>> bind (with a GI accession number) I blast against SPTrEMBL. This data will
>> give me a GI <-> SP accession number mapping for the dataset I am
>> interested in. 
>> 
>> It will also create (as a side effect) a whole load of data about close
>> homologues of the protein sequences available in BIND, which could be very
>> useful.
>> 
>> It will be easy to make a human subset of the data, for example
>> 
>> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=15117749&dopt=Abstract
>
>
>Thanks for your prompt reply. Yes it would be very useful to have this
>data. Since we already have the Uniprot id of human proteins, in which
>we are interested (and of course their names), it would be nice to know
>about their interactions with other human proteins. We have a set of
>ontologies which goes from the disease level to the cellular and
>subcellular level and this data will fit well with the lower level of
>granularity. Our end goal is to find the collaborations by which we
>wouldbe able to make a full-fledged carcinoma server, where various
>carcinoma related information can be searched from the name of disease,
>organ, drug, symptom, protein, cell, gene etc.

Cool!

You should also see the following links...

http://www.rfcgr.mrc.ac.uk/GenomeWeb/prot-interaction.html

including experimental protein interaction datasets and predictions.

Best of luck,
Dan.

>
>Kind Regards,
>Anand.
>
>Anand Kumar MBBS, PhD
>IFOMIS
>Faculty of Medicine
>University of Leipzig
>Härtelstraße 16-18
>04107 Leipzig
>Germany
>http://www.uni-leipzig.de/~akumar/
>
>
>
>
>
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