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6.2 years ago
Hello,
I would like to know if there is any software i could use to compare the genome of Phytophthora infestans and Phytophthora cinnamomi and deduce the differences in gene content
Thank you for your support
A.Chahed
I guess it depends on what you want to assess, of the gene content. Distribution? Function? Abundance of different families?
Thanks for your reply...
Yes i am looking for the genes present in P.inf but not in P.cinn (genes involved in carbohydrate metabolism)
Provided that the genomes are annotated (i.e. there are gene sets with gene sequences already ready), I think OrthoFinder is a good tool. It will get your sequences and search for orthologs. You'll get the groups of genes that are in 1 only, in 2 only, or in both. It can also run with multiple species (I used it with 7).
Thank you so much for your suggestions and support