Finding orthologs of 100 human genes in 44 insect transcriptomes

Question

[anuj2054]

Hello, I have a set of 100 UniRef proteins. I want to find orthologs of this set of proteins against a set of 44 transcriptomes. Would OrthoFinder help me in this ? I know OrthoFinder can find ortholog groups amongst the 44 transcriptomes themselves, but i need orthologs of he 100 Uniref proteins in particular for a phylogenetics study. Thanks, Anuj, University of Oklahoma

Answer 1

[david_emms]

Hi Anuj

I've just added a large amount of new functionality to OrthoFinder so it now infers orthologues as well as orthogroups. To do this it constructs orthogroups and then infers the gene tree for each orthogroup which is uses to identify orthologues (i.e. it does it the 'proper way' identified by Jean-Karim Henriche).

Also, there are indeed limitations of the reciprocal bast blast hit (RBH) approach and so that approach should be avoided (many genes will be missed if there have been gene duplications). OrthoFinder avoids this problem by using the RBHs to build up the skeleton of the orthogroup and then identifies the extra, duplicated genes that fit within this 'skeleton' so as to complete the orthogroups.

David

[mirza]

@david_emms Hi, Orthofinder is wonderful and definitely easy to use than other similar tools. Really helpful for biologist like us. I am able to run the tool successfully and got all the result files. But I want to know how to get the definition/ annotation of each orthogroup it sorts the protein sequences into? I am doing analysis with proteins predicted from whole genomes so its impossible to do it manually. Please guide me in his direction.

Answer 2

[Jean-Karim Heriche]

The proper way would be to build a phylogenetic tree, especially if you want to do a phylogenetics study. OrthoFinder and others use reciprocal best BLAST hits as a fast approximation but don't build a tree. If all you need are orthologs, you could also use this approach but be aware of its limitations.

Answer 3

[Giovanni M Dall'Olio]

• EggNog contains orthologs annotations for quite a good number of species. Not sure about how many insects are in there

• VectorBase curates annotation of organisms vectors of diseases. Maybe your species belong to the category. You should be able to get the orthologs from Tools > Biomart. Although you may have to ask them if they have a direct human-insect orthologs annotation