Hi Sandeep

Are you asking whether your orthologous protein of interest matches the currently accepted phylogenetics?

You have to keep in mind that all living organisms today can only estimate how your protein of interest may evolve. Whether is that the reality, we never know, unless you can extract the gene from fossils and sequence them.

I find this analogy pretty useful - To look at evolution from what is available now is like looking at the positions of leaves on a tree (and only that) and use it to draw out all the branches and trunk, which are "extinct" or non-existing already.

Similarly, humans do not evolve from chimpanzees but humans and chimpanzees evolve from a common human-chimp ancestor, which is non-existing now.

Maurice

Dear Ling, first of all thank you for your kind reply. I understood your suggestion. It's possible to track the course of evolution of a sequence, only with today's existing organisms whose sequences are available. Making my query clearer, I wanted to say I am in need to identify the relation between other similar and existing protein sequences in database. I wanted to develop a tree by selecting a set of protein sequences after performing BLASTp. I am actually new to phylogenics, but I can grasp if you provide me some ideas in this regard. I have another small doubt about how to get one most homologues sequence from one individual organism without repeated sequence from the same organism.

You may want to look at Multiple Sequence Alignment (http://www.ebi.ac.uk/Tools/msa/clustalo/)

Hello Sandeep,

It ultimately depends on what kind of analysis you are trying to perform. There is an online tool called ConSurf which takes a sequence and returns a colored map of amino acid conservation, which you can visualize using a molecular visualization software. The tool can be found here: (http://consurftest.tau.ac.il/). While I think this is not exactly what you are looking for, you may find the overview section useful, as it explains how the search is performed and how redundant sequences are removed. This could be a good place to start.

I hope this helps.

Max

Hello Sandeep

You may want to use MEGA (http://www.megasoftware.net/), very famous for phylogenetic analysis. It produces Multiple Sequence Alignment and Phylogenetic trees.

Your second question is unclear. Do you mean that there are several gene copies in a genome of interest?

Best

Lim