[Bioperl-l] locuslink - gene positions?
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.
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.
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