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Phylogeny tree from pdb data

[edited] Sorry for the broad question I had posted earlier. My problem is, I need to prove that my protein (DNA protein under starvation: 1vei) and ferritins (DPS is a member of the ferritin superfamily) might've evolved from a common ancestor.

Hence, which strategy to chose (sorry again about the elementary nature of my question, but, I am kind of starting to learn). Will a sequence alignment followed by a phylogenetic tree creation using MEGA will do? Or can I create it using conserved domain search in NCBI?

If you could point me to a simple enough read, detailing the theory behind the different methods, that would be invaluable for me right now.

Thanks for the responses.

Br, Praveen

[old stupid post] Hi, I have a PDB file and I am asked to generate a phylogenetic tree of my protein. I am very new to software biology (though I do have an iscb address) so, could you please help me.

From scratch, i.e. from "open windows then click internet explorer" would be nice.

Br, Praveen

alignment
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written by praveen.namboothiri • praveen.namboothiri

first problem: "open windows" ...why? does something smell? :)

second problem: "internet explorer" ... does this still exist? ;)

third problem: you haven't told us what you've tried/read/found/googled.

Try google first.

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written by BioinfGuru BioinfGuru

Ok...Because you are so new, I would suggest to avoid installing tools for this and just use a set of of online tools

Take a look here for some useful bioinformatics tools in evolutionary biology

you are right, a sequence alignment is one of the steps required before constructing the tree, however 2 sequences is not enough for a tree

So how do you think you will find more sequences (clue: homologues)?

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written by BioinfGuru BioinfGuru

From scratch

This isn't really within the scope of help in a forum - you need specific questions to get answers.

You won't get very far with a PDB file though. You need the amino acid sequence or the DNA sequence that encodes for that protein. You then need to find a number (the more the better usually) of related proteins (e.g. perhaps you want all the gyrB proteins from E. coli )

Once you have several related sequences, you can start to make phylogenies.

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written by Joe Joe

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