Overview of Genomic Tools for Circular Visualization in the Next-generation Genomic Sequencing Era
Alisha Parveen1, Sukant Khurana1, Abhishek Kumar1
11Medical Research Center, Medical Faculty of Mannheim, University of Heidelberg, Mannheim, Germany; 2Pharmacology Department, Central Drug Research Institute - Lucknow, Uttar Pradesh, India; 3Department of Genetics & Molecular Biology in Botany, Institute of Botany, Christian-Albrechts-University at Kiel, Kiel, Germany.
Current Genomics
|September 27, 2019
Summary
Genome sequencing generates vast data, necessitating effective visualization. This review summarizes circular genome visualization tools developed over 15 years to aid data interpretation.
Area of Science:
- Genomics
- Bioinformatics
- Data Visualization
Background:
- The human genome project and advancements in sequencing technologies have led to an exponential increase in genomic data.
- Effective methods for representing and interpreting this data are crucial for biological research.
- Circular genome visualization tools offer a simplified approach to understanding complex genomic datasets.
Purpose of the Study:
- To review and summarize the evolution of circular genome visualization tools.
- To provide a comprehensive overview of tools developed in the last 15 years.
- To aid researchers in selecting appropriate visualization methods for genomic data.
Main Methods:
- Systematic literature search for circular genome visualization tools.
- Analysis of tool development trends from 2003 to Q3 2018.
- Categorization and description of identified visualization tools.
Main Results:
- The development of circular genome visualization tools has accelerated, with 1-2 new tools emerging annually since the introduction of Circos.
- A wide array of tools has been developed, catering to diverse visualization needs in genomics.
- The review provides a consolidated reference of these tools up to September 2018.
Conclusions:
- Circular genome visualization tools are essential for interpreting large-scale sequencing data.
- The continuous development highlights the growing importance of effective genomic data representation.
- This summary serves as a valuable resource for researchers navigating the landscape of genome visualization tools.
Related Concept Videos
03:00Next-generation Sequencing
97.9K
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....
97.9K
02:54Evolutionary Relationships through Genome Comparisons
6.9K
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...
6.9K
03:36Genome Annotation and Assembly
20.5K
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.
20.5K
02:02Genomics
39.7K
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...
39.7K
00:58Genomic DNA in Eukaryotes
52.3K
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.
52.3K
03:21RNA-seq
11.8K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
11.8K