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BigDataBiology / macrel

Predict AMPs in (meta)genomes and peptides
http://big-data-biology.org/software/macrel
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what does CLP and CDP mean in the results? #70

Closed aslangabriel closed 1 month ago

aslangabriel commented 1 month ago

what does CLP and CDP mean in the results? There is no information on them, I just checked using chatgpt, it said that CLP (Classical Lipopeptides) and CDP (Cyclic Depsipeptides). I don't know if it is right?

celiosantosjr commented 1 month ago

Hi aslangabriel,

The nomenclature was supressed somehow during the versioning and was not mentioned largely in the paper. The terms referring to the AMP families are the following:

AMP family Description
CDP cationic disulfide peptide
CLP cationic linear peptide
ALP anionic linear peptide
ADP anionic disulfide peptide

They simply refer to the net charge and presence/absence of Cys/Met in the sequence.

Thanks for the question.

celiosantosjr commented 1 month ago

In fact, it was present in some previous versions of the manuscript in the biorxiv, but did not make to the final manuscript:

"AMP sequences are classified according to their hemolytic activity and classified into four different families by composition (Cationic or Anionic) and structure (linear or disulfide bond-forming). For convenience, duplicated sequences are clustered and output as a single entity. For calculating AMP abundance profiles, FACS uses Paladin (Westbrook et al., 2017) and NGLess (Coelho et al., 2019)."

aslangabriel commented 1 month ago

Subject: Thank You for Your Assistance with Macrel Software

Dear Mr. Santos-Jr.

I hope this message finds you well. I wanted to take a moment to express my sincere gratitude for your help with my questions regarding the Macrel software. Your insights and guidance were incredibly valuable and made a significant difference in my understanding of the program.

I appreciate the time you took to address my concerns and provide clear explanations. Your expertise has not only helped me resolve my issues but has also boosted my confidence in using the software moving forward.

Thank you once again for your support. I look forward to staying in touch and hope to reach out if I have more questions in the future.

Best regards,

Qi Feng

Celio Santos-Jr. @.***> 于2024年8月28日周三 06:32写道：

Closed #70 https://github.com/BigDataBiology/macrel/issues/70 as completed.

— Reply to this email directly, view it on GitHub https://github.com/BigDataBiology/macrel/issues/70#event-14036059130, or unsubscribe https://github.com/notifications/unsubscribe-auth/ALF4WUCHIFB6MYP5FOYKUCTZTT47HAVCNFSM6AAAAABND63RYSVHI2DSMVQWIX3LMV45UABCJFZXG5LFIV3GK3TUJZXXI2LGNFRWC5DJN5XDWMJUGAZTMMBVHEYTGMA . You are receiving this because you authored the thread.Message ID: @.***>

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