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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...
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.
Sanger Sequencing01:57

Sanger Sequencing

DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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Updated: May 24, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

Whole-genome alignment.

Colin N Dewey1

  • 1Biostatistics and Medical Informatics and Computer Sciences, Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI, USA. cdewey@biostat.wisc.edu

Methods in Molecular Biology (Clifton, N.J.)
|March 13, 2012
PubMed
Summary
This summary is machine-generated.

Whole-genome alignment (WGA) predicts evolutionary links between genomes. This challenging task is crucial for genome-wide analysis, driving advancements in phylogenetics and annotation.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
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An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

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Last Updated: May 24, 2026

Ultra-long Read Sequencing for Whole Genomic DNA Analysis
10:34

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

Published on: March 15, 2019

An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Whole-genome alignment (WGA) is essential for understanding evolutionary relationships at the nucleotide level across multiple genomes.
  • WGA integrates challenges from both collinear sequence alignment and gene orthology prediction.
  • The complexity and scale of whole genomes make WGA a significantly more difficult problem than its constituent tasks.

Purpose of the Study:

  • To define the meaning and significance of whole-genome alignment.
  • To provide a comprehensive overview of existing WGA methodologies.
  • To explore the challenges associated with evaluating whole-genome alignment tools.

Main Methods:

  • Review and synthesis of current whole-genome alignment algorithms.
  • Discussion of evaluation metrics and benchmarks for WGA tools.
  • Identification of key methodological challenges in the field.

Main Results:

  • WGA is a critical yet complex task with broad applications in genomics.
  • Numerous WGA methods have been developed, each with specific strengths and weaknesses.
  • Effective evaluation of WGA tools remains an open challenge.

Conclusions:

  • WGA is indispensable for genome-wide analyses like phylogenetic inference, genome annotation, and function prediction.
  • Addressing methodological challenges in WGA is crucial for leveraging vast genomic datasets.
  • Continued development in WGA methods and evaluation is necessary for advancing comparative genomics.