Dear all, I am studying a well known bacterial pathway. I've checked a couple of enzymes here (https://omabrowser.org/oma/) - I've found more than a thousand orthologs, but I need just orthologs in gram(+) bacteria. It's possible to do it manually, but I expect to spend a week on it. How can I do it computationally? OMA provides a lot of file-formats for its output. But I am pretty ignorant in HTML-files and Python, unfortunately. Thank you very much for any help! Natasha
As @Joseph Hughes points out, you will have to either use the REST API to search for the orthologs of your query genes and limit them to the gram-positive genomes (as far as my understanding goes these are essentially the Actinobacteria), or you parse the flat files that contain all the orthologs and filter the ones from your clade of interest. Both approaches require some scripting in your favorite language.
To get the set of Actinobacteria in OMA from the REST API you can use the following get-url: https://omabrowser.org/api/taxonomy/Actinobacteria/
Then, you can limit the orthologs (either pairwise or HOGs) to species belonging to set of Actinobacteria.