Question: How to obtain a list of proteins involved in organism specific pathways?
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gravatar for Alec Watanabe
10 months ago by
Alec Watanabe60 wrote:

Hello Biostars community,

I know there are some posts about pathways, KEGG and other tools but I do not quite think it is the same solution for me. Lets say I have a multifasta file containing protein sequences. What I want to do is analyze this set of proteins against an organism specific pathway database to find out which proteins are involved in metabolic pathways of the specific organism. Next, I want to compare the pathways or proteins to the pathway of the host (Homo sapiens) to identify proteins present only in pathogen pathways. Is there a way to obtain a list of the queried proteins involved in pathogen pathways (i.e. the queried proteins with "hits" in the specific pathway)? I tried KEGG PATHWAY with no success, maybe I did not know exactly how to operate the tool but I could not find a way to download the hits. Thank you.

pathways • 340 views
ADD COMMENTlink written 10 months ago by Alec Watanabe60

Want to try PathBLAST?

ADD REPLYlink modified 10 months ago • written 10 months ago by genomax76k

I'd love to. It seems like PathBLAST is a great tool. Unfortunately, the amount of queries that I have makes the tool, in its actual state, a little challenging. The FAQ section does mention a downloadable version of PathBLAST but its not implemented yet. Hopefully, soon we will have the chance to test a standalone version. Thank you for the suggestion and I will keep searching for an alternative.

ADD REPLYlink written 10 months ago by Alec Watanabe60
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