[Biodevelopers] Mapping between various protein indices

[Dan Bolser]

Glad I could help :)

The SRS method may be missing coverage because in the example I gave it is
linking explicitly to swissprot, 

http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[UNIPARC-refdbi:NP_001102]>SWISSPROT


The following...

http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?[UNIPARC-refdbi:NP_493453]>SPTREMBL


Is an example of how to use the explicit 'TREMBL' link. Despite the
name 'SPTREMBL' appears to only lookup TREMBL entries, so you should check
SPTREMBL and SWISSPROT in order to search for a mapping. If you end up
with only a few "un-mappable" entries it might be worth asking someone at
the NCBI/SRS/BBB about those entries.


The last resort is always blast, which is also supported by SeqHound, this
should allow you to find the new GI for a 'retired' GI, which could be the
major cause of missing GI's from the UNIPROT->GI mapping.

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




On Thu, 27 May 2004, Joke Reumers wrote:

>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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>
>
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