Question: Phylogenetic tree building from BlastP data
gravatar for danni_lynne
4.3 years ago by
danni_lynne0 wrote:

Hello everyone,

I just have a question regarding building phylogenetic trees.

I have a protein sequence that I have run through BlastP with several hits returned (250). I am wanting to build a phylogenetic tree with this data, but I am wondering if it is best to use the entire sequences of the hits or just the aligned sequence portion to complete the MUSCLE alignment and PHYML.

Which would be best and why?

Thank you so much for your time!

ADD COMMENTlink modified 4.3 years ago by Jean-Karim Heriche23k • written 4.3 years ago by danni_lynne0

While it is best to use the entire sequence as @Jean-Karim points out below, you should examine the blast hits in context. You may have picked up homologies to domains for example. If main protein of your interest is 50 AA and the hit points to a 500 AA protein then you would want to make your selection for MSA carefully.

ADD REPLYlink written 4.3 years ago by genomax91k
gravatar for Jean-Karim Heriche
4.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche23k wrote:

Use the entire sequences. Blast may have only picked up the most homologous regions and failed to align the less conserved parts which may nonetheless be picked up by a multiple alignment.

ADD COMMENTlink written 4.3 years ago by Jean-Karim Heriche23k
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