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Related Concept Videos

Next-generation Sequencing03:00

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.
Sanger Sequencing01:57

Sanger Sequencing

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...
RNA-seq03:21

RNA-seq

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 microarray-based...
DNA Microarrays02:34

DNA 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...
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...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...

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Informatic Analysis of Sequence Data from Batch Yeast 2-Hybrid Screens
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Published on: June 28, 2018

DDBJ launches a new archive database with analytical tools for next-generation sequence data.

Eli Kaminuma1, Jun Mashima, Yuichi Kodama

  • 1Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima 411-8510, Japan.

Nucleic Acids Research
|October 24, 2009
PubMed
Summary

The DNA Data Bank of Japan (DDBJ) released over 1.7 million genetic data entries and launched new services like the DDBJ Read Archive (DRA) and an annotation pipeline to improve data accessibility for researchers.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Data Archiving

Background:

  • The DNA Data Bank of Japan (DDBJ) is a critical resource for genetic information.
  • Data management and accessibility are crucial for advancing genomic research.

Purpose of the Study:

  • To report on the data releases and new services provided by DDBJ between July 2008 and June 2009.
  • To enhance user access to DDBJ's vast genetic datasets.
  • To introduce advancements in data visualization and annotation.

Main Methods:

  • Collection and release of over 1.7 million genetic entries.
  • Development of a Really Simple Syndication (RSS) service for daily data release announcements.
  • Implementation of a word cloud program for data visualization.
  • Launch of the DDBJ Read Archive (DRA) for next-generation sequencing data.
  • Introduction of the DDBJ Read Annotation Pipeline for semi-automatic data analysis.

Main Results:

  • DDBJ released 1,701,110 entries comprising 1,116,138,614 bases.
  • Notable data releases included endosymbiont genome sequences and Cap Analysis Gene Expression tags.
  • New services, including RSS, data visualization, DRA, and the annotation pipeline, were successfully launched.
  • The annotation pipeline offers basic (mapping, assembly) and high-level (structural, functional) analysis.

Conclusions:

  • The new DDBJ services significantly improve data accessibility and usability for researchers.
  • These advancements support a wide range of genomic research endeavors.
  • DDBJ continues to evolve as a leading repository for biological data.