[Bioperl-l] Sequence of Blast hit

[Jonathan Manning]

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