[BiO BB] GeneBank to SwissProt Mapping?

Anand Kumar anand.kumar at ifomis.uni-leipzig.de
Sat May 15 07:28:12 EDT 2004


> 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.

Kind Regards,

Anand Kumar MBBS, PhD
Faculty of Medicine
University of Leipzig
Härtelstraße 16-18
04107 Leipzig

More information about the BBB mailing list