Using tripal_synview without loading genome.fa and gff files to tripal

[songtaogui]

Hi,

I would like to set synteny view between my species (Organism A) and 30 other species (Organism B). However, it seems that the synview will work only if the gene fetures of both the A genome and the B genome can be found in tripal database.

Uploading gene features of these 30 species is time consuming and may influence data used for search modules. So I was wondering that if there is any sulotion to use tripal_synview without loading genome.fa and gff files to tripal, since the links of each organism B gene in the Display Syntenic Blocks Page is not necessary in my case.

Any suggestions and advices would be grateful.

Best wishes,
Songtao Gui

[kentnf]

Hi Songtao,
Currently, the tripal_synview is based on the tripal_feature. So, I have not idea how to make it work without loading gene features to the chado.

[athanasy-ljw]

Hi,

I would like to set synteny view between my species (litchi and longan) ,too . However , I don't know how to find the organism_id for the genome in chado database. How can I get the organism_id of litchi and longan ?

Any suggestions and advices would be grateful.
Best wishes,
Jiawei Li