OpenLB Open Library of Bioscience

PADS Arsenal: a database of prokaryotic defense systems related genes.

Yadong Zhang, Zhewen Zhang, Hao Zhang, Yongbing Zhao, Zaichao Zhang, Jingfa Xiao
Author Information
  1. Yadong Zhang: National Genomics Data Center, Beijing 100101, China.
  2. Zhewen Zhang: National Genomics Data Center, Beijing 100101, China.
  3. Hao Zhang: National Genomics Data Center, Beijing 100101, China.
  4. Yongbing Zhao: Department of Health Sciences Research, Mayo Clinic, Jacksonville, FL 32224, USA.
  5. Zaichao Zhang: Department of Biology, The University of Western Ontario, London, Ontario N6A 5B7, Canada.
  6. Jingfa Xiao: National Genomics Data Center, Beijing 100101, China.

Abstract

Defense systems are vital weapons for prokaryotes to resist heterologous DNA and survive from the constant invasion of viruses, and they are widely used in biochemistry investigation and antimicrobial drug research. So far, numerous types of defense systems have been discovered, but there is no comprehensive defense systems database to organize prokaryotic defense gene datasets. To fill this gap, we unveil the prokaryotic antiviral defense system (PADS) Arsenal (https://bigd.big.ac.cn/padsarsenal), a public database dedicated to gathering, storing, analyzing and visualizing prokaryotic defense gene datasets. The initial version of PADS Arsenal integrates 18 distinctive categories of defense system with the annotation of 6 600 264 genes retrieved from 63,701 genomes across 33 390 species of archaea and bacteria. PADS Arsenal provides various ways to retrieve defense systems related genes information and visualize them with multifarious function modes. Moreover, an online analysis pipeline is integrated into PADS Arsenal to facilitate annotation and evolutionary analysis of defense genes. PADS Arsenal can also visualize the dynamic variation information of defense genes from pan-genome analysis. Overall, PADS Arsenal is a state-of-the-art open comprehensive resource to accelerate the research of prokaryotic defense systems.

MeSH Term

Archaea
Archaeal Viruses
Bacteria
Bacteriophages
CRISPR-Cas Systems
DNA Restriction-Modification Enzymes
Databases, Genetic
Host-Pathogen Interactions
Software

Chemicals

DNA Restriction-Modification Enzymes

Links to CNCB-NGDC Resources

Database Commons: DBC007121 (PADS Arsenal)

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