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Related Concept Videos

Genome Annotation and Assembly03:36

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.
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...
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...
Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
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.
Synthetic Biology02:55

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

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

JEnsembl: a version-aware Java API to Ensembl data systems.

Trevor Paterson1, Andy Law

  • 1Division of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK. trevor.paterson@roslin.ed.ac.uk

Bioinformatics (Oxford, England)
|September 5, 2012
PubMed
Summary
This summary is machine-generated.

The JEnsembl Java API offers improved access to Ensembl data, enabling type-safe development of bioinformatics tools. This facilitates advanced analysis and visualization of genomic data from Ensembl and EnsemblGenomes.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Software Development

Background:

  • The Ensembl Project offers Perl APIs for accessing genomic data.
  • Perl is limited for large-scale applications and graphical interfaces.
  • A Java API is needed for enhanced bioinformatics tool development.

Purpose of the Study:

  • To develop a Java API (JEnsembl) for Ensembl data access.
  • To facilitate type-safe, modular, and object-oriented development.
  • To enable easier analysis and visualization of Ensembl data.

Main Methods:

  • Implementation of a Java API (JEnsembl).
  • Utilized a text-based configuration module for schema mapping.
  • Supported connections to current and archived Ensembl database instances.

Main Results:

  • JEnsembl provides data retrieval and manipulation for Ensembl and EnsemblGenomes.
  • The API architecture supports evolving database schema mappings.
  • Enables simultaneous connections to multiple database versions for comparative analysis.

Conclusions:

  • JEnsembl facilitates the development of advanced bioinformatics tools.
  • Improves analysis repeatability and enables 'through time' comparative studies.
  • Provides a platform for richer Ensembl data access and utilization.