Hi everyone
I want to identify orthologous genes in representative species I'm working on. So I performed Blast searches and pulled out the Best blast hits, I can see other people also do phylogenetic analysis. I am just confused, I have been reading literature and things are still not clear. Is Blast a starting point followed by phylogenetic analysis when you want to identify orthologous genes in certain species? My objective is to identify orthologs of Dicer, Argonaute and RNA depedent RNA polymerase in representative species of Armillaria.
BLAST alignments are indeed a good starting point for phylogenetic tree inference, but it's more an exploratory tool rather than a strict phylogenetic tree construction algorithm.
As I can get from what you've wrote you want to find orthologs, i.e homologous sequences originating in a common ancestor. What are you blasting in the first place ? ONE gene of SEVERAL species ? A SET of genes of those same species ? I'd suggest you to look for tools like MUSCLE or Clustal OMEGA as their doc will probably answer your questions.
By definition, orthologs are genes that derive from a common ancestor via speciation so strictly speaking, orthologs can only be inferred from a phylogenetic tree. Now because accurate reconstruction of a phylogenetic tree can be a computationally intensive task, various short cuts and approximations are often used as proxy. One such common approximation consists in forming orthologous groups by clustering genes based on similarity derived from best-reciprocal Blast hits.
But in your case, you could:
Check if your species of interest are in EnsemblFungi and whether orthologs have already been identified.
Take the HMM corresponding to your gene of interest from TreeFam or Ensembl Compara and perform a hmmsearch (part of the HMMER suite) of your fungi genomes
or conversely take the sequence of a candidate protein and use hmmscan to search the Ensembl or TreeFam database of HMMs to see which gene family your candidate most likely belongs to. Although a bit outdated, the Treefam website is convenient for a quick go at this and you can also visualize the protein in the tree.
