[Bioperl-l] Sequence of Blast hit

aditi gupta aditi9783 at yahoo.co.in
Mon Jun 7 09:42:24 EDT 2004

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 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?



Bioperl-l mailing list
Bioperl-l at portal.open-bio.org

Yahoo! India Matrimony: Find your partner online.

More information about the Bioperl-l mailing list