[BiO BB] GeneBank to SwissProt Mapping?

Dan Bolser dmb at mrc-dunn.cam.ac.uk
Tue May 18 09:38:45 EDT 2004


Blast derived mapping data is temporarily availible from 

http://interaction.mrc-dunn.cam.ac.uk/FTP/

Specifically 

http://interaction.mrc-dunn.cam.ac.uk/FTP/results.tab.gz

The format of which is

A	B	C	D
A	B	C	D
A	B	C	D
...

A = BIND GI
B = SWISS ID or TREMBL ACCN
C = Percent of sequence A which is identical to sequence B
D = Percent of sequence B which is identical to sequence A

A and B are sequence identifiers. Both C and D are required to check if
one sequence is a 'subsequence' of another.

e.g.

A       B               C       D

999601  G3P_THEMA       1       1
974697  Q59929          1       1
494170  Q7M0G1          1       0.4901
576205  PAR1_PAPHA      1       0.0541
196805  KAC_MOUSE       0.4472  1
896256  Q8RNV1          0.2713  1



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.
>
>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/
>
>
>
>
>
>_______________________________________________
>BiO_Bulletin_Board maillist  -  BiO_Bulletin_Board at bioinformatics.org
>https://bioinformatics.org/mailman/listinfo/bio_bulletin_board
>





More information about the BBB mailing list