[Gramene-extdev] Question about the 'NULL' protein domain in Arabidopsis

[Will Spooner]

Hi Greg,

Thanks for the feedback. We get the arabidopsis data the data directly 
in an ensembl database from NASC, so I will check back with them about 
these domains. It is unlikely that this will be fixed until NASC release a 
new database, unless we run the gramene pipeline on arabidopsis.

All the best,

Will

On Mon, 5 Nov 2007, Greg Brown wrote:

> Hi,
>
> We first found this 'NULL' domain type in our mirrored version 26. There are 
> two things we see that is strange.
>
> 1. There are dozens of Arabidopsis genes associated with the 'NULL' protein 
> domain that according to InterPro is not a valid domain. 
> http://www.gramene.org/Arabidopsis_thaliana/domainview?domainentry=NULL
>
> 2. If one of the peptides is selected with a 'NULL' domain the protview page 
> lists what apppears to be ALL protein domains, not just the ones assigned to 
> the particular protein. Here is an example; 
>
http://www.gramene.org/Arabidopsis_thaliana/
protview?transcript=AT1G02405.1-TAIR;db=core
>
> We assume there is some small systematic error with assignments of protein 
> domains. Do you anticipate a patched dataset for this version or will you 
> wait until version 27 to fix it? Thanks
>
> Greg Brown