Related Experiment Video
Updated: Jun 16, 2026
09:34
Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
[Design and construction of the platform for comparative genomics]
Na Liu1, Yun-bo Guo, Xian-he Sun
1Institute of Bioinformatics, School of Basic Medical Science, College of Biotechnology, Southern Medical University, Guangzhou 510515, China. liuna520@fimmu.com
Nan Fang Yi Ke Da Xue Xue Bao = Journal of Southern Medical University
|February 18, 2010
Summary
This study introduces a user-friendly genome comparison platform for analyzing viral and bacterial genomes. It facilitates comparative genomics by visualizing sequence alignments and identifying genomic differences.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Context:
- Comparative genomics is crucial for understanding evolutionary relationships and genetic diversity.
- Existing genome analysis tools often lack integrated visualization or user-friendly interfaces.
- The need for a versatile platform to compare diverse genomes efficiently is evident.
Purpose:
- To develop a browser/server-based platform for genome comparison and visualization.
- To integrate multiple alignment algorithms (MUMmer, LAGAN, Mauve) for versatile analysis.
- To provide an intuitive interface for data submission and results visualization.
Summary:
- The platform supports various input formats and alignment types (pairwise, multi-genome) for complete and draft genomes.
- It identifies regions of high similarity, mutations, and large-scale recombination.
- Case studies demonstrated its utility in analyzing influenza A virus and Mycobacterium species genomes.
Impact:
- Facilitates conventional comparative genomics studies through comprehensive resources and intuitive visualization.
- Enables researchers to explore evolutionary origins and genomic variations in pathogens.
- Aids in identifying key genetic differences between closely related bacterial species.
Related Concept Videos
02:54Evolutionary 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...
03:36Genome 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.
02:02Genomics
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...
00:58Genomic 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.
02:34DNA Microarrays
Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
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...