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Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Pathway code?

Hi is there a way to get all the fasta protein sequences from one KEGG pathway?

I want to get all the sequences from a Nematostella pathway:

nve04068    FoxO signaling pathway

Link for nve04068: http://www.kegg.jp/kegg-bin/show_pathway?nve04068+NEMVE_v1g162441

It would be something similar to this post, but not sure it is possible to use the pathway code instead of the orthology code.

Thanks

kegg pathway fasta
• 5,124 views • link
updated by Ram Ram • written by catagui • catagui

1 answer

You can try my Python script.

Summary

  1. Find 100 orthology ids for the pathway id "ko04068" with this link
  2. Find many gene ids for each orthology id with links like this.
  3. Retrieve FASTA sequence for a gene id: http://www.genome.jp/dbget-bin/www_bget?-f+-n+n+aml:100467269

Related questions

Extracting List Of Genes Associated With A Pathway In Kegg

• 0 views • link
updated by Ram Ram • written by Kamil Kamil

Thanks for the script Kamil I will try it out.

• 0 views • link
updated by Ram Ram • written by catagui • catagui

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