Related Experiment Video
Updated: Sep 19, 2025
04:58
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
Published on: December 13, 2024
2.9K
SVbyEye: a visual tool to characterize structural variation among whole-genome assemblies
David Porubsky1,2, Xavi Guitart1, DongAhn Yoo1
1Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, United States.
Bioinformatics (Oxford, England)
|June 6, 2025
Summary
A new R package, SVbyEye, visualizes genome structural variations. This tool aids in characterizing complex structural variants and understanding their formation mechanisms.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Routine generation of highly contiguous genome assemblies is now possible.
- Complex structural variations and rapid evolutionary turnover are being discovered.
- Efficient visualization tools are needed to compare genome structures.
Purpose of the Study:
- To develop an open-source R package for visualizing and annotating sequence-to-sequence alignments.
- To facilitate the characterization of complex structural variants.
- To aid in resolving the mechanisms underlying structural variant formation.
Main Methods:
- Developed SVbyEye, an R package.
- Implemented functionalities for processing sequence alignments.
- Integrated visualization of sequence-to-sequence alignments.
Main Results:
- SVbyEye enables visualization and annotation of sequence alignments.
- The package facilitates the characterization of complex structural variants within sequence homology.
- The tool aids in understanding the formation mechanisms of structural variants.
Conclusions:
- SVbyEye provides an efficient tool for evaluating structural differences between genomes.
- The package supports the discovery and characterization of novel structural variations.
- SVbyEye is an open-source resource available on GitHub and Zenodo.
Related Concept Videos
03:36Genome Annotation and Assembly
19.4K
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.
19.4K
02:26Comparing Copy Number Variations and SNPs
18.0K
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%...
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%...
18.0K
02:54Evolutionary Relationships through Genome Comparisons
6.2K
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...
6.2K
01:11Genome-wide Association Studies-GWAS
14.4K
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...
GWAS does not require the identification of the target gene involved in...
14.4K
03:00Next-generation Sequencing
92.8K
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....
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
92.8K
01:57Sanger Sequencing
758.2K
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...
758.2K