tag pangenome

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Débora P. de Oliveira

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Aug 16, 2021, 4:18:27 PM8/16/21
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Hi everyone,

I'm going back to using anvi'o now and I would like to know if there is any way to export all the genes I found in the pangenome for an analysis in GhostKoala (KEGG), I would also like to ask if there is any way to tag the genes that found in analyzes outside the anvi'o such as bacteriocins, antibiotic resistance genes, etc. Graphically it would be an interesting figure for my work.

Thank you for your attention,
Debora

A. Murat Eren

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Aug 16, 2021, 9:06:02 PM8/16/21
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Hey Debora,

You can export gene sequences from the original contigs databases, annotate them in any way you wish, and then import your annotations into contigs databases again before regenerating your pangenome.

Essential anvi'o programs to do this include the following:


I hope this helps.



Best wishes,
Meren.


--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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Débora P. de Oliveira

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Aug 17, 2021, 8:06:06 PM8/17/21
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Hi Meren, 

Thank you so much for answering so quickly.
I'm sorry, but I can't access the links (not found for both)
Is it available for everyone?

Best wishes,
Debora

Mike Lee

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Aug 17, 2021, 8:10:55 PM8/17/21
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Hey there, Debora :)

Something odd must have happened, but they work without the “/“ at the end 👍 

https://merenlab.org/m/anvi-get-sequences-for-gene-calls

-Mike

--
Michael D. Lee, PhD
Blue Marble Space Institute of Science
NASA Ames Research Center
astrobiomike.github.io <- bioinformatics for beginners
GToTree <- phylogenomics for all

On Aug 17, 2021, at 5:03 PM, Débora P. de Oliveira <dehpre...@gmail.com> wrote:


Hi Meren, 

Thank you so much for answering so quickly.
I'm sorry, but I can't access the links (not found for both)
Is it available for everyone?

Best wishes,
Debora

To view this discussion on the web visit https://groups.google.com/d/msgid/anvio/CAK5_LafqCg04ug_7wAocyBkHzgKwszHCnLQici6x2FMYmo02RQ%40mail.gmail.com.


--
Débora Preceliano de Oliveira
Nutricionista e Mestre em Ciência dos Alimentos
Telefone:  (11) 98285-2091

--
Anvi'o Paper: https://peerj.com/articles/1319/
Project Page: http://merenlab.org/projects/anvio/
Code Repository: https://github.com/meren/anvio
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Mike Lee

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Aug 17, 2021, 8:15:19 PM8/17/21
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ugh, changed the text but not the links, ha

these work

Débora P. de Oliveira

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Aug 17, 2021, 8:19:51 PM8/17/21
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Hey Mike, 

Thank you SO much. 
I tried it in several ways, except without "/" (you are a genius and you saved me)

Best wishes,
Debora
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