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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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In 1928, bacteriologist Frederick Griffith worked on a vaccine for pneumonia, which is caused by Streptococcus pneumoniae bacteria. Griffith studied two pneumonia strains in mice: one pathogenic and one non-pathogenic. Only the pathogenic strain killed host mice.
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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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PGAweb: A Web Server for Bacterial Pan-Genome Analysis.

Xinyu Chen1, Yadong Zhang2,3,4, Zhewen Zhang2,3

  • 1Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.

Frontiers in Microbiology
|September 7, 2018
PubMed
Summary
This summary is machine-generated.

A new web tool, PGAweb, simplifies bacterial pan-genome analysis for researchers. It offers intuitive functions for exploring genomic diversity and evolution, aiding in understanding microbial genomes.

Keywords:
bacterial pan-genome analysisgenome dynamics visualizationgenome structure interpretationorthologous gene identificationweb server

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Area of Science:

  • Bioinformatics
  • Microbial genomics
  • Computational biology

Background:

  • The exponential growth of microbial genome data necessitates advanced bioinformatic tools for comprehensive pan-genome analysis.
  • Existing tools may lack user-friendliness or comprehensive features for analyzing genomic diversity across bacterial species.

Purpose of the Study:

  • To introduce PGAweb, a novel, user-friendly, web-based platform designed for bacterial pan-genome analysis.
  • To provide researchers with integrated tools for exploring orthologous clustering, pan-genome profiling, and evolutionary dynamics.

Main Methods:

  • PGAweb integrates two core modules: PGAP (Pan-Genome Analysis Pipeline) and PGAP-X.
  • The platform offers customizable functions including orthologous clustering, pan-genome profiling, sequence variation analysis, and functional classification.
  • Interactive visualization methods are employed to illustrate genomic structural dynamics and sequence diversity.

Main Results:

  • PGAweb facilitates intuitive understanding of bacterial genome evolution and structural dynamics.
  • The tool enables one-click parameter settings for streamlined analysis.
  • Key features include comparative genomics, evolutionary analysis, and functional annotation of pan-genomes.

Conclusions:

  • PGAweb addresses the demand for accessible and powerful bacterial pan-genome analysis tools.
  • Its user-friendly interface and comprehensive features support research into microbial genome evolution and diversity.
  • The platform is freely available, promoting wider adoption in the scientific community.