6.5 years ago by
San Francisco, California
Please try BioMart again, because I just toyed around with the Ensembl Gene 61 mart and it does return parts of the flanking sequence.
- go to http://www.biomart.org/biomart/martview
- select 'ENSEMBL GENES 61' as database
- select 'Homo sapiens genes' as dataset
- click on 'Attributes' and then on the 'Sequences' radio-button
- for the example I selected 'Flank (Gene)'
- in 'Upstream flank' I entered 10 just as an example
- click on 'Filters'
- select chromosome 12
- as base pairs I entered 131780000 and 131783000 (which spans over ENSG00000248703, 131780658 to 131782517)
- click on 'Results'
The FASTA result is:
If you click on 'XML', you are given a small XML-document that you can use to query the mart programmatically (see http://www.biomart.org/user-docs.pdf). For this example, the XML looks like this:
<?xml version="1.0" encoding="UTF-8"?>
<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
<Filter name = "upstream_flank" value = "10"/>
<Filter name = "chromosome_name" value = "12"/>
<Filter name = "end" value = "131783000"/>
<Filter name = "start" value = "131780000"/>
<Attribute name = "ensembl_gene_id" />
<Attribute name = "ensembl_transcript_id" />
<Attribute name = "gene_flank" />
If you click on 'Perl', BioMart generates some Perl code for you as an alternative to running the XML-queries. It should be fairly easy to modify the Perl code to your needs.