What alternative method would recommend for conducting gene ontology analysis?

Question

[mathavanbioinfo]

Hi,

I am conducting gene ontology analysis for a de novo assembled genome of plant species. After genome assembly and repeat masking, I used EggNOG Mapper to obtain the GO terms. I planned to utilize the WEGO gene ontology annotation tool for the analysis. This tool computes and provides output in the form of bar diagrams for cellular component, molecular function, and biological process. Unfortunately, I am currently unable to access this tool. Can you suggest an alternative method for performing gene ontology analysis with the provided input sample?

Input file (tab separated)

g631.t1 GO:0000045                                           
g631.t1 GO:0000407         
g631.t1 GO:0005575      
g631.t1 GO:0005622                                                                                                                                    
g631.t1 GO:0005623                          
g631.t1 GO:0005737                                                                                                                                                              
g631.t1 GO:0005783                                                                                                                                                     
g631.t1 GO:0005789                                                                                                                                           
g631.t1 GO:0006810                                                                                                                       
g631.t1 GO:0006887

Answer 1

[dthorbur]

There are dozens of well cited tools that can be used to calculate GO enrichment. The best place to look for tools is on search engines and you can look through recent papers to see what others in your field are using.

Personally, I like g:Profiler2 for non-model organisms since you can create a custom universe to test against quite easily once you figure out how to format the GMT file. Note, this is a pretty simple enrichment implementation, and unless I missed an update, it isn't as robust as tools that use hierarchical structure of GO terms to estimate enrichment.