On 14 Nov 2007, at 07:32, David M. Goodstein wrote:
I was wondering if there are any shortcuts that enable UCSC table
browser-style intersection queries in BioMart. The typical
application would be to grab all the genes that overlap a given set of
sequences (e.g., ESTs) aligned to the reference genome. Or does one
need to retrieve all the spans for the alignments in questions and
then directly query BioMart for overlap with each span?
Hi David,
we are currently testing an additional functionality in mart where you
could intersect two gene lists e.g.
gene list A (uniprot) and gene list B (entrez genes) and retrieve an
intersection between them based
on mapping to the same core ids ei ensembl. is t his what you are after
or do you mean something else?
a.
regards,
-David
David M. Goodstein
Computational Genomics Group
Joint Genome Institute
Lawrence Berkeley National Lab
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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