Frequenty Asked Questions - BioMart

How can I download sequences and their correspondent genomic coordinates using BioMart?

BioMart is provided for Ensembl Plants, Ensembl Metazoa, Ensembl Protists and Ensembl Fungi. You can download gene sequences and flanking regions in FASTA from BioMart by choosing 'sequences' under the 'attributes' and selecting one of the following: unspliced (Transcript or Gene), flank (Transcript or Gene), flank-coding region (Transcript or Gene), 5. UTR, 3. UTR, Exon sequences, cDNA sequences, Coding sequence and protein. You can choose to download either upstream or downstream gene flanking sequence. You can expand the 'Header Information' option under 'attributes' and choose the gene coordinates as gene start (bp) and gene end (bp). More details on how to use BioMart can be found here. For non-gene centric downloads, please use the 'Export data' option on the Ensembl Genomes browser (see here), the region report tool (under the link Tools, for example in Ensembl Bacteria: http://bacteria.ensembl.org/tools.html) or the Ensembl Genomes Perl API (for example in Ensembl Fungi:http://fungi.ensembl.org/info/docs/api/index.html).

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