AGONOTES: A Robot Annotator for Argonaute Proteins.

Journal: Interdisciplinary sciences, computational life sciences
PMID: 31741225

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.

Authors

  • Lixu Jiang
    Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China.
  • Min Yu
    From the Division of Laboratory Medicine, Department of Pathology, University of Virginia School of Medicine and Health System, Charlottesville. Dr Yu is currently located in the Department of Pathology and Laboratory Medicine, University of Kentucky Medical Center, Lexington.
  • Yuwei Zhou
    Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China.
  • Zhongjie Tang
    Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 637111, China.
  • Ning Li
    Department of Respiratory and Critical Care Medicine, Center for Respiratory Medicine, the Fourth Affiliated Hospital of School of Medicine, and International School of Medicine, International Institutes of Medicine, Zhejiang University, Yiwu, China.
  • Juanjuan Kang
    Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.
  • Bifang He
    Medical College, Guizhou University, Jiaxiu Road, Huaxi Zone, Guiyang 550025, P. R. China.
  • Jian Huang
    Center for Informational Biology, University of Electronic Science and Technology of China, No. 2006, Xiyuan Ave, West Hi-Tech Zone, Chengdu 611731, P. R. China.

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