[ensembl-dev] LRG_gene sequences missing - Ensembl 59

[Pontus Larsson]

  Hi,

Within Ensembl, the LRG sequences can be found by searching for e.g. the 
LRG identifier or the HGNC name of a gene for which an LRG record 
exists. Since the LRG sequences are not part of the genome assembly, 
they have their own dedicated display, e.g. 
http://www.ensembl.org/Homo_sapiens/LRG/Summary?lrg=LRG_1. The LRG 
display is till very much under development and currently does not have 
the same functionality as the genome assembly display but we are 
constantly working on improving the functionality. You can e.g. view the 
LRG sequence annotated with the transcripts that are defined on the LRG 
along with projections of SNPs. The transcript annotations and sequences 
are also obtainable through the Perl API.

At the moment, you can not view the gene annotations from the genome 
assembly in the context of LRGs but for the upcoming Ensembl release 60, 
we aim to project and display this information. Note that at the moment, 
this projection is also available within the LRG XML files that are 
available for download and display on the LRG website, e.g. 
http://www.lrg-sequence.org/LRG/LRG_1.

Any further suggestions on useful functionality on the LRG display 
within Ensembl are most welcome!

Also, note that if you search for an LRG on the LRG website and follow 
the link to the Ensembl browser, there will be a GFF file attached to 
the display that indicates the structure of the LRG transcript(s) on the 
genome assembly (e.g. 
http://www.ensembl.org/Homo_sapiens/Location/View?r=17:48259457-48284000&contigviewbottom=url:ftp://ftp.ebi.ac.uk/pub/databases/lrgex/.ensembl_internal/LRG_1.xml.gff=labels).

Thanks
/Pontus Larsson - Ensembl Variation


On 13/10/2010 18:53, Bio X2Y wrote:
> Hi,
>
> The LRG sequences gene annotations seem to be dropped from Ensembl 59. 
> Is this intentional?
>
> Thanks.
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

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