Question: Kegg- kaas equivalent in Biocyc
1
gravatar for charly.blanche.t
5.0 years ago by
United States
charly.blanche.t20 wrote:

Hello all,

Can somebody pls tell me what is the equivalent of Kaas (Kegg) in Metacyc/Biocyc? 

KAAS (KEGG Automatic Annotation Server) provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

My goal is to generate metabolic pathways from my sample fasta files.

 

Thank you

rna-seq • 1.9k views
ADD COMMENTlink modified 5.0 years ago by Prakki Rama2.2k • written 5.0 years ago by charly.blanche.t20
0
gravatar for Prakki Rama
5.0 years ago by
Prakki Rama2.2k
Singapore
Prakki Rama2.2k wrote:

After submitting the fasta files to KAAS, you are provided a link (with html,text). When html page is clicked, you can "Exec" the page, which will lead you to pathway list. By clicking any pathway, you can generate the pathway and genes you were able to capture from the pathway. Is that what you are looking for? For example, after submitting my fasta file and checking Glycolysis pathway, my pathway looks like this. (link might expire little later)
 

ADD COMMENTlink modified 5.0 years ago • written 5.0 years ago by Prakki Rama2.2k

Thank you Praki. What you are describing, I have already done that in Kegg. Now I want to genrate the same pathway graph but  using Biocyc. Why I am moving to Biocyc is because, in Kegg, nodes in the graph are sometimes EC number but quite often, the EC numbers can be the edges. This makes it difficult for me to capture the pathways as graph since it will involve taking the dual in some cases...

ADD REPLYlink written 5.0 years ago by charly.blanche.t20

I would also be interested if you find some answer. I have not dealt with Biocyc before.

ADD REPLYlink written 5.0 years ago by Prakki Rama2.2k

Hey @charly.blanche.t , were you able to figure this out? I am looking for a way to generate a graph using the BioCyc data.

ADD REPLYlink written 2.7 years ago by kandoigaurav120
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