[Bioperl-l] Getting Genomic Sequences using Bioperl

Brian Osborne bosborne11 at verizon.net
Mon Oct 27 15:13:46 EDT 2008


I'm CCing the Bioperl list in case someone has suggestions.

If I were faced with this task I'd either use the ENSEMBL API  
(described on the Getting Genomic Sequences page) or the eutils API at  
NCBI or I'd take a look at the UCSC Genome Browser. There are people  
who are experts at using the eutils API in this list, perhaps they'll  
have some specific suggestions about how to get genomic sequences  
starting with Gene ids.

Brian O.

On Oct 27, 2008, at 2:24 PM, Benson, Craig C wrote:

> Hi Brian,
> I was wondering if you knew of a way to set the species genome and  
> build when using  Bio::DB::GenBank (to get the sequence given  
> specific coordinates) or when using  Bio::DB::EntrezGene (to get the  
> coordinates)?  For instance, I have a list of ~300 genes (w/ Gene  
> ID) and I'd like to use a perl script to retrieve the dna sequence  
> 50bp up and down stream from the transcription start site of these  
> genes from both the human genome and the mouse genome.  I'm assuming  
> that the example code on the bioperl documentation page for "Getting  
> Genomic Sequences" (http://www.bioperl.org/wiki/HOWTO:Getting_Genomic_Sequences 
> ) defaults to the most recent human genome. Is that correct?  Is  
> there a better way to retrieve these two sequences besides using  
> bioperl?
> Thanks!
> Craig C. Benson, MD
> Med-Peds Residency Program
> University of Rochester Medical Center

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