How to make ortholog table

Question

[beginner123]

I would like to construct an ortholog table of 10 proteins from 100 species, as shown below, but I don't know how to do it. I am not good at programming, so if possible, I would like to use a web server, but most of these web servers have query limitations. Does anyone know of any useful tools or methods for constructing ortholog table?

Answer 1

[Mensur Dlakic]

You may want to try OrthoMCL using a website:

https://orthomcl.org/orthomcl/app

Or as a stand-alone program:

https://orthomcl.org/common/downloads/software/v2.0/

[dariober]

I would consider orthoMCL deprecated in favor of orthofinder for a number of reasons. Orthofinder should be better in finding orthologues. Also, OrthoMCL repository hasn't been updated in 6 years and the last time I tried it was quite a pain to install it.

[beginner123]

Thank you all! I will try orthofinder. By the way, does anyone know anything about the usability of SonicParanoid?

Answer 2

[Matthias Zepper]

You can retrieve the Orthologues for up to 6 species with Ensembl Biomart.

• Use the data mining tool, choose Ensembl Genes 106 as the dataset and select Human genes (or whatever organism you would like to have as reference).
• On the left, click on Attributes and choose Homologues (Max select 6 orthologues) in the radio button selector to the right.
• Down below, uncheck the fields for Gene ID and Transcript ID respectively versions and instead check the box next to Protein Stable ID.
• Then select the organisms for which you would like to get the accession number, e.g. Giant panda protein stable ID and so on.
• Use the filter tab to select only the IDs / proteins of interest.
• When finished, click on the results button in the upper left corner and download the data, e.g. as TSV.

There are also ways to query Biomart e.g. directly from R, which is clearly easier if you wish to select all orthologs from more species than 6, but then you would need to code.