what is the best way to find ortholog protein in other bacterial strains ?
you can use orthofinder, which is easy to run and produces many useful comparative genomics results as well as phylogenetic trees inculuding species tree and ortholog trees.
here is the link
The best way to find orthologs is to read some posts that have already discussed a similar problem and do some reading.
A few of the posts on Biostars that discuss the same are:
What is the best method to find orthologous genes of a species?
Ortholog Detection tool
Finding the orthologs in the genome
Simplest way is to do a bi directional blast !!
My group prepared a very nice tool based on KEGG ( see https://dariusz-izak-doktorat.github.io/ )
When I pressed the link, I received 404-error - no requested file.
With all due respect, while this could be useful, that website is so messy and looks unprofessional, I would not invest effort in going through it. Strongly recommend a makeover if this is really a working solution.
I tried to enter — I received 404-error — no requested file.
Sorry about it. It should be https://dariusz-izak-doktorat.github.io/
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