How can I retrieve data from the Ensembl database?
Please have a look at our tutorial which you can download here. If you are looking for a certain gene or marker, try FAQ no. 1 and/or 2. If you are interestred in complex queries in the Ensembl database, like e.g. retrieving all genes with a certain domain, or downloading 1 kb upstream of the transcription start of all predicted genes, try Biomart. If you want to download sequence data from Ensembl, you can either try the mouse-over on the blue sequence box in the middle of the contigview window. The ‘export this file’ option leads you to the Export data window. Please note that this option will only give you the part of the sequence that was used in the assembly. If you want to download the sequence of a whole finished clone and it overlaps with it’s neighbours, then only the non-overlapping part will be returned in the exported file. For the whole sequence of a finished clone, please use the ‘EMBL source file’ option from the mouse-over.
Please have a look at module 2 of our tutorial. If you are looking for a certain gene or marker, try FAQ no. 1 and/or 2. If you are interested in complex queries in the Ensembl database, such as retrieving all genes with a certain domain, or downloading 1 kb upstream of the transcription start of all predicted genes, try Biomart, which is also described in module 2 of our tutorial. If you want to download sequence data from Ensembl, you can click on the blue box representing the contig or clone itself. The ‘Export’ option leads you to the Export data window. Please note that this option will only give you the part of the sequence that was used in the assembly. If you want to download the sequence of a whole finished clone and its overlaps with its neighbours, then only the non-overlapping part will be returned in the exported file. For the whole sequence of a finished clone, please look up the entire entry in EMBL using its accession.
