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Using Pathway tools for unannotated genome

asked 2019-11-14 09:40:03 -0500

anonymous user


Hello, I have reconstructed bacterial genomes (from metegnomic sequencing) and I want to better annotate their genes and to find pathways. I can of course predict ORFs. Is you tools (coupled with metacyc for example), can help with annotating genomes?

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answered 2019-11-15 02:08:48 -0500

Suzanne Paley gravatar image

No, sorry. In order to get useful information, you should annotate the genome before feeding it in to Pathway Tools. Our PathoLogic tool relies on the functional information in the annotation file to assign enzymes to reactions, so without that information, you won't get any reactions or pathways. There are other annotation pipelines out there -- our tools are intended to operate downstream of those.

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Asked: 2019-11-14 09:40:03 -0500

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Last updated: Nov 15 '19