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AGONOTES: A Robot Annotator for Argonaute Proteins

  • Lixu Jiang
  • Min Yu
  • Yuwei Zhou
  • Zhongjie Tang
  • Ning Li
  • Juanjuan Kang
  • Bifang He
  • Jian HuangEmail author
Original research article
  • 79 Downloads

Abstract

The argonaute protein (Ago) exists in almost all organisms. In eukaryotes, it functions as a regulatory system for gene expression. In prokaryotes, it is a type of defense system against foreign invasive genomes. The Ago system has been engineered for gene silencing and genome editing and plays an important role in biological studies. With an increasing number of genomes and proteomes of various microbes becoming available, computational tools for identifying and annotating argonaute proteins are urgently needed. We introduce AGONOTES (Argonaute Notes). It is a web service especially designed for identifying and annotating Ago. AGONOTES uses the BLASTP similarity search algorithm to categorize all submitted proteins into three groups: prokaryotic argonaute protein (pAgo), eukaryotic argonaute protein (eAgo), and non-argonaute protein (non-Ago). Argonaute proteins can then be aligned to the corresponding standard set of Ago sequences using the multiple sequence alignment program MUSCLE. All functional domains of Ago can further be curated from the alignment results and visualized easily through Bio::Graphic modules in the BioPerl bundle. Compared with existing tools such as CD-Search and available databases such as UniProt and AGONOTES showed a much better performance on domain annotations, which is fundamental in studying the new Ago. AGONOTES can be freely accessed at http://i.uestc.edu.cn/agonotes/. AGONOTES is a friendly tool for annotating Ago domains from a proteome or a series of protein sequences.

Keywords

Argonaute protein Gene silencing Genome editing Similarity search Protein recognition Domain annotation 

Abbreviations

Ago

Argonaute protein

AGONOTES

Argonaute Notes

AaAgo

Aquifex aeolicus argonaute

eAgo(s)

Eukaryotic argonaute protein(s)

ePIWIs

ePIWI proteins

hAgo1

Human argonaute 1

hAgo2

Human argonaute 2

KpAgo

Kluyveromyces polysporus argonaute

L1 domain

Linker1 domain

L2 domain

Linker2 domain

MID domain

Middle domain

MpAgo

Marinitoga piezophila argonaute

mAgo2

Mouse argonaute 2

non-Ago(s)

Non-argonaute protein(s)

N domain

N-terminal domain

NgAgo

Natronobacterium gregoryi argonaute

pAgo(s)

Prokaryotic argonaute protein(s)

PAZ domain

PIWI–Argonaute–Zwille domain

PIWI domain

P element–induced wimpy testis domain

PfAgo

Pyrococcus furiosus argonaute

pPIWIs

pPIWI proteins

RsAgo

Rhodobacter sphaeroides argonaute

SpAgo1

Schizosaccharomyces pombe argonaute 1

TtAgo

Thermus thermophilus argonaute

Notes

Acknowledgements

The authors are grateful to the anonymous reviewers for their valuable suggestions and comments, which have led to the improvement of this paper. In addition, thanks to Hui Yang for valuable discussions and suggestions. This work was supported by the National Natural Science Foundation of China [Grant no. 61571095] and the China Postdoctoral Science Foundation Grant [Grant no. 2019M653369].

Compliance with Ethical Standards

Conflict of Interest

The authors declare no conflict of interest, financial or otherwise.

Human and Animal Rights

No animals/humans were used for studies that are the basis of this research.

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Copyright information

© International Association of Scientists in the Interdisciplinary Areas 2019

Authors and Affiliations

  1. 1.Center for Informational Biology, School of Life Science and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
  2. 2.School of MedicineGuizhou UniversityGuiyangChina

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