[Bioperl-l] locuslink - gene positions?

Barry Moore barry.moore at genetics.utah.edu
Tue Aug 31 14:10:07 EDT 2004

Chromosome coordinates for genes and other features are available from 
UCSC genome browser either as file downloads from the ftp site, or as 
table downloads from the table browser.


hz5 at njit.edu wrote:

>I believe that there is a flatfile in MapView ftp directory, some kind of md 
>file have coordinate of genes relative to both chromosome and contigs.
>Quoting "Fontaine, Burr R" <bfontain at iupui.edu>:
>>I am trying to mirror portions of Locuslink and have figured out how to
>>get all of the data elements I need from the locuslink module except for
>>the gene starting postion (in bp coordinates). Chromosome coordinates
>>would be best but contig coordinates are OK if there is a way to convert
>>them. I've looked at the location modules but don't see any obvious
>>answers there. Can someone help me figure out the best way to do this?
>>Thanks in advance for your help.
>>Burr Fontaine
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>Haibo Zhang, PhD student
>Computational Biology, NJIT & Rutgers University
>Center for Applied Genomics, PHRI
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org

Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

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