[Bioperl-l] Sequence of Blast hit
bmb9jrm at bmb.leeds.ac.uk
Mon Jun 7 09:48:12 EDT 2004
No, actually I haven't used Biomart. I actually found the Ensembl API
easy enough to use itself. Actually, it was the lack of species present
in GenBank which promted the question.
On Mon, 2004-06-07 at 14:42, aditi gupta wrote:
> hi jon,
> have you tried Ensembl' new tool BIOMART?
> it might be of some help.......what do you want exactly?just the
> exons?then choose 'exon information' after running biomart.but biomart
> is available for very few species....
> Jonathan Manning <bmb9jrm at bmb.leeds.ac.uk> wrote:
> Hi All,
> I have been using BLAST to locate nucleotide sequences to the
> genome. I
> have then been using the Ensembl API to extract information
> based on the
> results. I'm doing something now where I really only need the
> genomic sequence, and from organisms other than those
> represented in
> Ensembl. The trouble is that when I BLAST with a cDNA, the
> HSPs clearly only match exonic regions, so I need to get the
> information from somewhere else. I don't want to retrieve the
> contig file.
> Is there an easy way to download a subsequence of
> sequence without the whole file?
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