[Bioperl-l] How to get from gi/ref/gb to genomic coordinates ?

Chris Fields 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
> http://fungal.genome.duke.edu/
> 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  
> want
> to do more complex analysis later :-)
>
> Thank you very much!
>
> Rainer

If the data is available in GenBank you could run the BLAST searches  
at NCBI and limit the search with an Entrez query:

http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#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?

chris


More information about the Bioperl-l mailing list