-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 BioMart cannot currently use the results from one query or subquery as a filter to apply to another query, which is what I think you're asking? (You would want to obtain genomic coordinates for the ESTs as your subquery then use those as input to some kind of 'overlaps' filter in the main query to return the genes).
Also, the public BioMart marts do not currently have any overlap-style filters. You would probably need to define your own mart containing genes and genomic coordinates for this purpose and in it create two filters - gene_start_position with operator <=, and gene_end_position with operator >= - then pass the EST end coordinate to the gene_start_position filter, and the EST start coordinate to the gene_end_position filter. cheers, Richard 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? > > regards, > -David > > > David M. Goodstein > Computational Genomics Group > Joint Genome Institute > Lawrence Berkeley National Lab > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFHOrWd4C5LeMEKA/QRAnPQAJsH8mA+VNcy5n4b2X7I6h+GKWC16QCeKBZe a+dpEBrS+dQdnIMpmhIv+dk= =HhKI -----END PGP SIGNATURE-----
