[Bioperl-l] How to get from gi/ref/gb to genomic coordinates ?
cjfields at uiuc.edu
Thu Feb 1 12:55:27 EST 2007
On Feb 1, 2007, at 6:54 AM, Rainer Machne wrote:
> Barry and Jason,
> thanks for your quick and very helpful replies.
> I guess we should have done (or repeat) our blast search at
> to get better mapping from proteins to genomes ?
> As I retrieved all my proteins via whole genome blasts we should find
> (most of) them in the genbank files ... a good opportunity for me to
> learn some Bioperl and the other packages you mentioned in case we
> to do more complex analysis later :-)
> Thank you very much!
If the data is available in GenBank you could run the BLAST searches
at NCBI and limit the search with an Entrez query:
Most (all?) genome files are tagged as complete
I'm not sure but there might be a way of doing this via
Bio::Tools::Run::RemoteBlast. Jason, any ideas?
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