[Bioperl-l] Sequence of Blast hit

Jonathan Manning 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?
> http://www.ebi.ac.uk/biomart/index.html
> 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....
> -aditi
> 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
>         matching
>         genomic sequence, and from organisms other than those
>         represented in
>         Ensembl. The trouble is that when I BLAST with a cDNA, the
>         resulting
>         HSPs clearly only match exonic regions, so I need to get the
>         sequence
>         information from somewhere else. I don't want to retrieve the
>         entire
>         contig file.
>         Is there an easy way to download a subsequence of
>         contig/chromosome
>         sequence without the whole file?
>         Thanks,
>         Jon
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