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RHdb links to UniGene

Peter Rice pmr at sanger.ac.uk
Thu Sep 3 13:04:12 EST 1998


t.j.keen at leeds.ac.uk (T. Jeffrey  Keen) writes:

> Does anyone know a method to search the Radiation Hybrid database for
> entries relating to a specific UniGene cluster, without knowing the
> accession number for the particular EST from which the mapping STS was
> derived.
> 
> What I (and others) want to do, is given any member of a UniGene cluster,
> to find the RHdb entry for any EST which forms part of that cluster.

Yup - SRS can do this easily. RHDB can be linked to DBEST which can
be linked to UNIGENE. Seqrching Unigene goes through *all* the ESTs on
the way to RHDB.

For example, RHDB entry RH100 is linked to dbEST Id 51416 (accnum: D20789)

Other ESTs in UniGene cluster Hs.5801 include:

dbEST Id:       234388
GenBank Acc:    R57651
dbEST Id:       435767
GenBank Acc:    N34374
dbEST Id:       444417
GenBank Acc:    N42835

You can search using the Sanger Centre SRS server. Other SRS servers
may also have these databases linked.

http://www.sanger.ac.uk/srs5/

Select database UNIGENE, search for R57651 as sequenceAcc
(returns one hit to Hs.5801)

Then use the "link" button, and select RHDB (low down under "Mapping).
This returns RH100 and RH11501 (both accnum D20789, different RH panels).

There is a shortcut:

http://www.sanger.ac.uk/srs5bin/cgi-bin/wgetz?[unigene-acc:R57651]>rhdb

(substitute your favourite accession number)

or, from a Unigene cluster:

http://www.sanger.ac.uk/srs5bin/cgi-bin/wgetz?[unigene-id:hs.5801]>rhdb


-- 
----------------------------------------------------------------------
Peter Rice                | Informatics Division, The Sanger Centre,
E-mail: pmr at sanger.ac.uk  | Wellcome Trust Genome Campus,
Tel: (44) 1223 494967     | Hinxton, Cambridge, CB10 1SA, England
Fax: (44) 1223 494919     | URL: http://www.sanger.ac.uk/Users/pmr/



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