Question: GO enrichment analysis on Non-model Organism
1
gravatar for EVR
4.2 years ago by
EVR570
Earth
EVR570 wrote:

Hi,

I am working on non-model organism for which there is no proper genome or transcriptome available. So to find the GO, everytime we have to depend on BLASTx analysis hits.

So for these kind non-model organism, is it possible to GO enrichment analysis ?  

ADD COMMENTlink modified 4.2 years ago by Jean-Karim Heriche21k • written 4.2 years ago by EVR570

Sure, once you've mapped predicted GO terms via BLAST, you can do your enrichment as normal. You might want to consider doing best reciprocal blast hits to cut down on false assignments due to paralogs.

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by pld4.8k
1
gravatar for Jean-Karim Heriche
4.2 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k wrote:

The standard approach is to transfer GO annotations by orthology. If you're dealing with an animal, you can use TreeFam to insert a protein into a gene tree and infer its orthologs, either via the web site or using the API.

ADD COMMENTlink written 4.2 years ago by Jean-Karim Heriche21k
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