How to find a conserved regions for a protein by phylogentic analysis tree
Hi , Iam working on GPR146 , which an orphan receptor and My project is to do phylogenetic analysis for this protein to give insight into the relationship and the pharmacological proprieties of rhodopsin like GPCRs . The idea is to find the conserved regions of this type of GPCR and it can help to predict ligand binding sites. Does any one knows how to find conserved regions from phylogenetic analysis ?
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See Asaf answer in this post:
A: How Can I Interpret A Multiple Sequence Alignment?
This presentation is a general theory in case you need it:
http://bldg6.arsusda.gov/benlab/Cairo_course/5_Motif_and_Trees_GS.pdf
This one below may also be helpful:
How To Extract Conserved Regions From A Large Number Of Sequences
and see similar posts on the right panel.
Thank you very much