[Bioperl-l] genome position mapping of RefSeq IDs

Chris Fields cjfields at illinois.edu
Wed Feb 25 15:54:28 EST 2009

Bio::Coordinate?  I haven't used it myself but IIRC it is capable of  
doing something along these lines.


On Feb 25, 2009, at 2:40 PM, Robert Citek wrote:

> Hello all,
> I have a list of RefSeq IDs for which I can parse out all the
> annotation (e.g. exons, SNPs, etc.).  For this one project, I need the
> same coordinate information relative to the genome rather than the
> transcript.  Is such mapping information available?  Or are pieces
> available so that I can string them together?
> A simple use case would be for me to query a dataset with a RefSeq and
> it will return the genomic coordinates of all introns.
> I've looked at the mapping information at
> ftp://ftp.ncbi.nih.gov/gene/DATA, which gets me close but seems to be
> missing some parts.  Or is that what I'm looking for and I just don't
> see how the pieces fit?
> Thanks in advance for any pointers in the right direction.
> Regards,
> - Robert
> On Wed, Oct 22, 2008 at 2:54 PM, Chris Fields  
> <cjfields at illinois.edu> wrote:
>> You can 'epost' in increments if you have more IDs, up to 1000-2000  
>> I think.
>> Beyond that, you should probably use one of the mapping files  
>> located in
>> the ftp.ncbi.nih.gov/gene/DATA folder and just use it locally  
>> (initially
>> index the data with DB_File, search using a tied hash, etc).
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