Question: Is There Any Way To Retrieve Protein Sequences In Fasta Format using a Kegg Pathway code?
0
gravatar for catagui
4.7 years ago by
catagui30
Miami, FL, USA
catagui30 wrote:

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

It would be something similar to this post: C: Is There Any Way To Retrieve Genes' Sequences In Fasta Format Using The Kegg Ort , but not sure it is possible to use the pathway code instead of the orthology code. 

Thanks

kegg fasta pathway • 2.9k views
ADD COMMENTlink modified 4.7 years ago by Kamil2.0k • written 4.7 years ago by catagui30
3
gravatar for Kamil
4.7 years ago by
Kamil2.0k
Boston
Kamil2.0k wrote:

You can try my Python script.

Summary

  1. Find 100 orthology ids for the pathway id "ko04068" with this link: http://www.genome.jp/dbget-bin/get_linkdb?-t+orthology+pathway:ko04068
  2. Find many gene ids for each orthology id with links like this: http://www.genome.jp/dbget-bin/get_linkdb?-t+genes+ko:K00922
  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

ADD COMMENTlink modified 4.5 years ago • written 4.7 years ago by Kamil2.0k

Thanks for the script Kamil I will try it out. 

ADD REPLYlink written 4.7 years ago by catagui30
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