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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.

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 Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.

Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

Gene Families

Gene Families

Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...

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Related Experiment Video

Updated: May 23, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

Community gene annotation in practice.

Jane E Loveland¹, James G R Gilbert, Ed Griffiths

¹Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK. jel@sanger.ac.uk

Database : the Journal of Biological Databases and Curation

|March 22, 2012

Summary

Community annotation tools enable remote collaboration for genomic data, making gene set creation more accessible beyond model organisms. This approach enhances annotation consistency and quality control for valuable genomic reference data.

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Last Updated: May 23, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Manual genomic data annotation is crucial for accurate reference gene sets but is costly, limiting its application to model organisms.
Existing annotation tools face challenges in scalability and accessibility for broader community involvement.
Remote access to annotation tools is essential for enabling global collaborative efforts.

Purpose of the Study:

To introduce novel tools and strategies for community-driven genomic data annotation.
To address the limitations of cost and accessibility in creating comprehensive gene sets.
To facilitate remote collaboration for improving the accuracy and scope of genomic annotations.

Main Methods:

Development and implementation of the 'Blessed' annotator and 'Gatekeeper' approach.
Utilizing the Otterlace/ZMap genome annotation tool for remote community annotation.
Adoption of specific strategies for ensuring annotation consistency and quality control.

Main Results:

Successful remote community annotation of genomic data is demonstrated.
The 'Blessed' annotator and 'Gatekeeper' approach facilitate collaborative efforts.
Strategies for quality control and viewing enhance the reliability of the annotation process.

Conclusions:

Community annotation, enabled by remote tools, significantly expands the potential for generating accurate genomic reference gene sets.
The Otterlace/ZMap tool, with the 'Blessed' and 'Gatekeeper' system, provides a viable framework for large-scale, collaborative genome annotation.
This approach overcomes traditional cost and accessibility barriers, paving the way for broader genomic data refinement.