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Can we use MeMe motif output result and prepare tree from motif

hello all,

I am using MeMe motif analysis server for my protein sequences analysis, in result i am getting html file with block diagram of motif but i can not download the block diagram so can i use output file motif for phylogenetic tree construction.

sample file attached can we download that block diagram by any means. http://meme-suite.org/doc/examples/meme_example_output_files/meme.html

Please suggest me.

meme motif phylogenentic tree block diagram
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written by Vinay Singh • Vinay Singh

You want to use the motif for tree construction? Why/How?

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written by Joe Joe

Yes because all protein sets have some motifs in common and some have unique set of motif, so to separate sets with similar sets of motif we can cluster them.

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written by Vinay Singh • Vinay Singh

You'd be better off using HMM profiles or similar for an alignment. If you're adamant about doing it your way, you can use Biopython to get a Posititon-Specific-Score-Matrix which will give you proportions of each residue at each position, which is basically the information that's in a MeMe logo.

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written by Joe Joe

Thank you for the information, can you tell any method to download that block diagram obtained in MeMe analysis.

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written by Vinay Singh • Vinay Singh

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