[Bioperl-l] Sequence of Blast hit

[aditi gupta]

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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