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Related Concept Videos

Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.7K
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...
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Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Next-generation Sequencing03:00

Next-generation Sequencing

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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....
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Genome Annotation and Assembly03:36

Genome Annotation and Assembly

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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.
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Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Related Experiment Video

Updated: Dec 7, 2025

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
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NGS_SNPAnalyzer: a desktop software supporting genome projects by identifying and visualizing sequence variations

Dong-Jun Lee1, Taesoo Kwon2, Chang-Kug Kim3

  • 1Genomics Division, National Institute of Agricultural Science, 370 Nongsaengmyeong-ro, Jeonju, 54874, Republic of Korea. leemoses1004@gmail.com.

Genes & Genomics
|September 27, 2020
PubMed
Summary

NGS_SNPAnalyzer is a new, user-friendly software for detecting genetic sequence variations from next-generation sequencing (NGS) data. It offers automated analysis and visualization, improving accuracy and accessibility for researchers.

Keywords:
GenomicsNext-generation sequencingPipelineVariant identificationWhole-genome sequencing

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying sequence variations, like single nucleotide polymorphisms, is crucial for understanding genetic diseases and breeding.
  • Existing genome project consortiums offer standard operating procedures, but human error can lead to result discrepancies.
  • Standardization in sequence variation detection is needed to ensure reliable and reproducible results.

Purpose of the Study:

  • To develop a standardized, user-friendly tool for sequence variation detection.
  • To assist researchers without extensive bioinformatics training in analyzing next-generation sequencing (NGS) data.
  • To create an automated graphical pipeline for efficient variant analysis.

Main Methods:

  • Developed NGS_SNPAnalyzer, a desktop software with a fully automated graphical pipeline.
  • Implemented using JavaFX (version 1.8) for cross-platform compatibility (Windows and Ubuntu Linux).
  • Integrated tools for variant calling, annotation, quality control, mapping, and filtering.

Main Results:

  • NGS_SNPAnalyzer provides comprehensive functionalities from NGS data processing to variant visualization.
  • The software offers both pre-set and customizable analysis pipelines.
  • It features a user-friendly graphical interface, installable on any Java-supported OS.

Conclusions:

  • NGS_SNPAnalyzer simplifies NGS data analysis with an easy-to-use interface.
  • Benchmark tests show superior performance compared to other open-source tools.
  • The software enhances accessibility and reliability in genetic variation detection.