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Related Concept Videos

Genome Annotation and Assembly03:36

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
Genomics02:02

Genomics

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...
Next-generation Sequencing03:00

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features.
Genomic DNA in Eukaryotes00:58

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
Protein Complex Assembly02:41

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types.  Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

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Updated: May 12, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies
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Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Metagenomic Assembly and Gene Prediction.

Bo Li1, Xue Yang2, Tongyi Zhao2

  • 1Guangdong Basic Research Center of Excellence for Ecological Security and Green Development, School of Ecology, Environment and Resources, Guangdong University of Technology, Guangzhou, China. libo01@gdut.edu.cn.

Methods in Molecular Biology (Clifton, N.J.)
|May 10, 2026
PubMed
Summary
This summary is machine-generated.

Metagenomic assembly and gene prediction are crucial for microbiome analysis. These processes transform raw sequencing data into valuable insights for understanding microbial communities and reconstructing genomes.

Keywords:
ContigGene predictionHybrid sequencingMetagenomic assembly

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Area of Science:

  • Microbiology
  • Bioinformatics
  • Genomics

Background:

  • Metagenomic assembly and gene prediction are foundational steps in microbiome research.
  • Quality-controlled reads are essential for accurate downstream analyses.

Purpose of the Study:

  • To outline core metagenomic assembly strategies.
  • To introduce gene prediction and nonredundant gene catalog construction.
  • To highlight assembly quality evaluation metrics.

Main Methods:

  • Discussing per-sample versus co-assembly approaches.
  • Comparing short-read versus hybrid assembly methods.
  • Detailing gene prediction from assembled contigs.

Main Results:

  • Contigs and gene sets are generated as fundamental outputs.
  • Assembly quality is evaluated using key parameters and metrics.
  • Nonredundant gene catalogs represent community coding potential.

Conclusions:

  • Metagenomic assembly and gene prediction are vital for MAG reconstruction.
  • These steps provide essential input for taxonomic and functional annotation.
  • The chapter serves as a basis for advanced microbiome analyses.