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Shuyib / Phylogenetic-tree-study

Estimating Phylogenetic trees using six microorganisms 16S rRNA gene with Unsupervised Learning, web based tools and Molecular Evolutionary Genetics Analysis MEGA7
https://github.com/Shuyib/Phylogenetic-tree-study/wiki
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Use KEGG or something else to find out the function of the motifs found by MEME. Refer to biopython. #28

Closed Shuyib closed 1 year ago

Shuyib commented 1 year ago

https://www.genome.jp/kegg/pathway.html

Shuyib commented 1 year ago

KEGG can also be run in biopython. Please write a function to interact with it better.

Shuyib commented 1 year ago

Actually might just want to use BLAST for this as opposed to KEGG. Specifically, UniProt to determine what the protein is about

Shuyib commented 1 year ago

I have added the potential functions for the motifs found using UniProt BLAST. See the results in meme_out3/6 in the TSV files. The lower the E value the better and remember we are looking at microbes. Thus, functions on that scope are better. Might want to do more queries maybe look for 9, 12, 18 motifs in future.