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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
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problem of AMG number #51

Closed mujiezhang closed 3 years ago

mujiezhang commented 3 years ago

Hello, I got a question in VIBRANT results about AMG number. I found the number of AMG is 404 in VIBRANT_annotations_virus.tsv and VIBRANT_AMG_individuals_virus.tsv, but the number changed to 600 in VIBRANT_AMG_pathways_virus.tsv and the pdf of AMGs barplot. I wonder the reason for the difference. Thanks.

KrisKieft commented 3 years ago

Hi,

This was an original oversight on my part for how KEGG parses their data. KEGG will allow individual KO numbers to be parts of multiple pathways if the protein/enzyme can have multiple functions, or if that function can be a part of multiple pathways. VIBRANT identified 404 AMGs but some of those AMGs can have multiple functions, or possible functions, that increase the pathway presence to 600.

mujiezhang commented 3 years ago

Really thanks for your helpful reply! I got it.

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发件人: Kris Kieft 发送时间: 2021年7月2日 23:39 收件人: AnantharamanLab/VIBRANT 抄送: mujiezhang; Author 主题: Re: [AnantharamanLab/VIBRANT] problem of AMG number (#51)

Hi, This was an original oversight on my part for how KEGG parses their data. KEGG will allow individual KO numbers to be parts of multiple pathways if the protein/enzyme can have multiple functions, or if that function can be a part of multiple pathways. VIBRANT identified 404 AMGs but some of those AMGs can have multiple functions, or possible functions, that increase the pathway presence to 600. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.