Question: Functional Annotation Of Orthomcl Groups?
gravatar for SK
6.7 years ago by
SK110 wrote:

One of the cons of OrthoMCL is "OrthoMCL groups do not have function annotations". Could someone suggest me how to annotate the OrthoMCL groups?

ADD COMMENTlink modified 6.7 years ago by SES8.3k • written 6.7 years ago by SK110
gravatar for SES
6.7 years ago by
Vancouver, BC
SES8.3k wrote:

I think you may be confusing the purpose of OrthoMCL, which is unrelated to functional annotation. The goal is to define orthogroups with which can try to work out orthology relationships, and then analyze patterns of evolution in a comparative way, usually in light of gene function or evolutionary rate. You did not say what type of data you have, but for many species, you can search for orthogroups by a term or function. If you included one of these species, or a species with annotations, you could carry over annotations from those reference species. If you are analyzing a group of non-model species, then you will have to generate these annotations yourself.

If you want to assign a putative function to your genes, run HMMER or InterProScan. The results can be mapped directly to GO terms, if that is what you are interested in.

ADD COMMENTlink written 6.7 years ago by SES8.3k
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