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

Question

[Vinay Singh]

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.

[Joe]

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

[Vinay Singh]

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.

[Joe]

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.

[Vinay Singh]

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