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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.
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...
Gene Duplication and Divergence02:37

Gene Duplication and Divergence

The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are characterized.
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...
Structure of a Gene01:30

Structure of a Gene

A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Analyzing and Building Nucleic Acid Structures with 3DNA
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Published on: April 26, 2013

Gene3D: merging structure and function for a Thousand genomes.

Jonathan Lees1, Corin Yeats, Oliver Redfern

  • 1Department of Biochemistry and Molecular Biology, University College London, Gower St, London WC1 6BT, UK.

Nucleic Acids Research
|November 13, 2009
PubMed
Summary
This summary is machine-generated.

The Gene3D resource now offers enhanced accuracy and interactive displays for structural domain family assignments across millions of proteins and genomes. This updated database integrates diverse functional and structural annotations for comprehensive protein analysis.

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Area of Science:

  • Structural bioinformatics
  • Genomics
  • Protein domain analysis

Background:

  • The Gene3D resource provides structural domain family assignments for proteins.
  • Previous versions required improvements in accuracy and user interface.

Purpose of the Study:

  • To present the significant improvements made to the Gene3D resource over the past two years.
  • To highlight the enhanced accuracy, interactive display, and expanded data coverage of Gene3D.

Main Methods:

  • Utilized a hidden Markov model library derived from the CATH structural domain hierarchy.
  • Applied the in-house DomainFinder 3 algorithm to refine protein sequence matches into multi-domain architectures.
  • Integrated domain assignments with external data from Gene Ontology, KEGG, Pfam, and eggNog.

Main Results:

  • Gene3D now covers over 1100 genomes and nearly 10 million proteins with improved accuracy.
  • The Gene3D website offers a richer interactive display for exploring protein and gene information.
  • Domain assignments are integrated with extensive functional, structural, and family annotations.

Conclusions:

  • The updated Gene3D resource provides a more accurate and comprehensive platform for structural domain analysis.
  • The enhanced website facilitates detailed investigation of proteins, genes, and large biological datasets.
  • Gene3D offers valuable services for researchers, including visualization tools and data access via SOAP services.