9.2 years ago by
Yes there is if your organism is in Ensembl - BioMart. Here is how you'd use the web interface, assuming that you want human sequences:
- Go to BioMart and click MARTVIEW
- Select database = Ensembl Genes 57
- Select dataset = Homo sapiens genes
- Click "Filters" to the left and open the "Gene" selection
- From the dropdown box, select the IDs that you want to use (e.g. UniProt/TrEMBL)
- Either paste your list in the box or upload the file
- Click "Attributes" to the left, select the "Sequences" radio button and open the "Sequences" tab
- Select what type of sequence (e.g. unspliced transcript)
- Click "Results" (in menu bar, top-left of page)
This will return the first 10 sequences. You can download the rest as a file. There is also programmatic access to Ensembl: Perl API, biomaRt for R Bioconductor.
If this doesn't work for you, the Bioperl library should be able to retrieve sequences given IDs.