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Related Concept Videos

Genomics02:02

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...
Evolutionary Relationships through Genome Comparisons02:54

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 Screens02:46

Genetic Screens

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.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Genome-wide Association Studies-GWAS01:11

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...
Imaging Biological Samples with Optical Microscopy01:18

Imaging Biological Samples with Optical Microscopy

Optical microscopy uses optic principles to provide detailed images of samples. Antonie van Leeuwenhoek designed the first compound optical microscope in the 17th century to visualize blood cells, bacteria, and yeast cells. In 1830, Joseph Jackson Lister created an essentially modern light microscope. The 20th century saw the development of microscopes with enhanced magnification and resolution.
In optical microscopy, the specimen to be viewed is placed on a glass slide and clipped on the stage...

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Mapping Mammalian 3D Genome Interactions with Micro-C-XL
11:41

Mapping Mammalian 3D Genome Interactions with Micro-C-XL

Published on: November 3, 2023

OmicBrowse: a Flash-based high-performance graphics interface for genomic resources.

Akihiro Matsushima1, Norio Kobayashi, Yoshiki Mochizuki

  • 1Bioinformatics and Systems Engineering division (BASE), RIKEN (The Institute of Physical and Chemical Research), 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.

Nucleic Acids Research
|June 17, 2009
PubMed
Summary
This summary is machine-generated.

OmicBrowse is an open-source genome browser for managing multiple genome annotation datasets. This scalable system reduces costs by enabling collaborative data access and integration for researchers.

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

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Area of Science:

  • Bioinformatics
  • Genomics
  • Data Management

Background:

  • Managing and accessing diverse genome annotation datasets is complex.
  • Collaborative research requires efficient sharing of both published and unpublished data.
  • Existing systems often incur high maintenance costs for private data sharing.

Purpose of the Study:

  • To introduce OmicBrowse, a scalable genome browser system.
  • To facilitate secure, multi-user access to numerous genome annotation datasets.
  • To reduce data maintenance costs for collaborative research.

Main Methods:

  • Developed OmicBrowse as an open-source genome browser.
  • Implemented a system for regulating multi-user data access to datasets.
  • Integrated support for DAS1 (Distributed Annotation System) imports and exports.
  • Provided OmicDownload server for interactive dataset selection and filtering.

Main Results:

  • OmicBrowse enables users to create integrative views of their datasets.
  • The system significantly reduces maintenance costs associated with private data sharing.
  • Supports seamless data exchange with worldwide Internet site servers via DAS1.
  • OmicDownload facilitates efficient data retrieval and filtering.

Conclusions:

  • OmicBrowse offers a scalable and cost-effective solution for genome annotation data management.
  • The platform enhances collaborative research by providing controlled access to integrated datasets.
  • OmicBrowse is a valuable open-source tool for the bioinformatics community.