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Genomics

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...

Genome-wide Association Studies-GWAS

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...

Evolutionary Relationships through Genome Comparisons

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...

Genetic Screens

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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
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Next-generation Sequencing

Next-generation Sequencing

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.

Genome Annotation and Assembly

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.

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

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Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Helga Thorvaldsdóttir¹, James T Robinson, Jill P Mesirov

¹Broad Institute, 7 Cambridge Center 301B-5057, Cambridge, MA 02142, USA.

Briefings in Bioinformatics

|April 21, 2012

Summary

This summary is machine-generated.

The Integrative Genomics Viewer (IGV) handles large genomic datasets for researchers. It offers high-performance visualization for diverse sequencing and array data, supporting integrated analysis.

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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Genomic data analysis relies heavily on effective visualization tools.
Large, diverse datasets from sequencing and array profiling pose significant challenges to existing visualization software.
There is a need for tools that can efficiently handle and integrate various genomic data types.

Purpose of the Study:

To introduce the Integrative Genomics Viewer (IGV) as a solution for visualizing large and heterogeneous genomic datasets.
To highlight IGV's capabilities in supporting integrative genomic studies, including diverse data types and clinical information.
To emphasize IGV's design for high-performance, user-friendly exploration of both public and private genomic data.

Main Methods:

Development of a high-performance genome data viewer (IGV).
Implementation of support for array-based and next-generation sequencing data.
Integration of features for handling large, heterogeneous datasets and clinical/phenotypic data.
Optimization for efficient data loading (local and remote) and visualization on standard desktop systems.

Main Results:

IGV provides efficient handling of large, diverse genomic datasets.
The viewer ensures a smooth and intuitive user experience across all genome resolutions.
IGV effectively integrates array-based, next-generation sequencing, and clinical/phenotypic data.
High-performance data visualization and exploration are achieved on standard desktop systems.

Conclusions:

IGV is a powerful, high-performance tool for visualizing and exploring complex genomic data.
Its integrative capabilities and user-friendly design support researchers in analyzing their own data.
IGV is freely available, promoting broader accessibility for genomic data analysis.