[Bioperl-l] locuslink - gene positions?

Stefan Kirov skirov at utk.edu
Wed Aug 25 17:01:11 EDT 2004

I think you are right- there are no coordinates and there should be 
(contig coordinates of course). Actually the contig accession number is 
in the object as a DBLink object. I don't think DBLink is a suitable 
place for the contig coordinates. Another problem with LLink module is 
that it permits null values for the primary ID for sime DBLink objects 
(LLID 218 for examples). This is definitely a bug.
I guess you can request this to be added to the module- file a bug 
report. I can probably take a look at that but not today, sorry.
You can also check Ensembl API- it may be more straightforward for your 
needs. Something that I am doing (this is not an advertisement) might be 
also helpful: genereg.ornl.gov/gkdb, but we are struggling with some 
update issues, so I wouldn't use it right now.
Have fun,

Fontaine, Burr R wrote:

>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

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