[Biodevelopers] Mapping between various protein indices

[Joke Reumers]

Hi,

Thanks for the input, I have been able to retrieve a lot more data this way!
The first method doesn't give a full mapping however, but I will try the
second one this weekend and see how that goes. The so-called IPI-index
doesn't come near your solutions (http://www.ebi.ac.uk/IPI/IPIhelp.html), so
you've been a great help!

Thanks,
Joke


-----Original Message-----
From: biodevelopers-admin at bioinformatics.org
[mailto:biodevelopers-admin at bioinformatics.org] On Behalf Of Dan Bolser
Sent: Tuesday, May 25, 2004 3:26 PM
To: biodevelopers at bioinformatics.org
Subject: Re: [Biodevelopers] Mapping between various protein indices


On Tue, 25 May 2004, Joke Reumers wrote:

>Hello,
>
>Maybe a bit out of scope on this mailing list, but I'm trying to find a 
>complete mapping between NCBI RefSeq (of Genbank gi) indices and 
>SwissProt/TrEMBL accessions. The best I could find so far is the IPI 
>index, but this seems far from complete. Anyone any better ideas?


Hi, I had this exact same problem recently! The 'best' two solutions I
finally found were;

1) Use SRS to map from RefSeq -> uniPark -> SwissProt

(can't find where to get unipark from directly)

2) Use SeqHound to get SwissProt from GI.

I was shown the SRS method, e.g.

http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[UNIPARC-refdbi:NP_001102]%3ESWISS
PROT


And I got the following instructions on the use of SeqHound...

If you want a list of GI's that have *exactly* the same sequence as your
input protein GI, then you could use
 

'SHoundRedundantGroup'

http://www.blueprint.org/seqhound/api_help/apifunctsdet.html#SHoundRedundant
Group
 

The Perl version of this takes a GI as input and then returns a list of
GI's.  You could use SHoundSeqIDFromGi (or SHoundSeqIDFromGiList) to find
the Swiss-Prot sequence.


Using either of these should get you a full mapping. Let me know how you get
on, 


Dan.


>
>Thanks in advance,
>
>Joke Reumers
>
>
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