Multiple Proteome comparision

Question

[Mehmet]

Dear All:

I have a proteome data of a non model organisms. I want to see which protein families are expanded in the proteome data compared to another related or non related species. For this:

Which procedure should I follow?

Thank you.

Answer 1

[Juke34]

Have a look to clusterisation tools such as OrthoMCL, InParanoid, OrthoDB and so one. Once the clusters built, you can analyse for each cluster the number of putative Orthologs of your species compared to the others.

[Mehmet]

Hi:

I have used orthoMCL to find ortholog proteins in 12 proteome files. I mean I want to search some protein domains in 12 proteome files, such as neuropeptides, peptides etc. to find which protein domains are expanded in my species proteome files. For this, what kind of analyses and tools should I use?

[Juke34]

To add domain information to your proteins in order to compare their domain content you should launch Interproscan5.