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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.

Evolutionary Relationships through Genome Comparisons

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...

Genomic DNA in Eukaryotes

Genomic DNA in Eukaryotes

Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.

Multi-species Conserved Sequences

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...

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Related Experiment Video

Updated: Mar 19, 2026

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Published on: December 22, 2017

The Ensembl gene annotation system.

Bronwen L Aken¹, Sarah Ayling², Daniel Barrell³

¹European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK bronwen.aken@ebi.ac.uk smjsearle@yahoo.co.uk.

Database : the Journal of Biological Databases and Curation

|June 25, 2016

Summary

This summary is machine-generated.

The Ensembl gene annotation system provides comprehensive gene sets for over 70 vertebrate species. It uses sequence alignment to build and refine gene models, ensuring accurate genomic data for research.

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

Published on: May 28, 2021

Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

The Ensembl gene annotation system is a widely used resource in genomics.
Accurate gene annotation is crucial for understanding genome function and evolution.

Purpose of the Study:

To detail the Ensembl gene annotation process.
To highlight the system's application in annotating diverse vertebrate species and human/mouse GENCODE gene sets.

Main Methods:

Alignment of biological sequences (cDNAs, proteins, RNA-seq) to target genomes.
Construction and filtering of candidate transcript models.
Generation of automatic alignment-based annotation for GENCODE gene sets.

Main Results:

Annotation of over 70 vertebrate species.
Generation of automatic annotation for human and mouse GENCODE gene sets.
A detailed description of the Ensembl annotation pipeline.

Conclusions:

The Ensembl system provides a robust and scalable method for gene annotation.
The generated gene sets are publicly available via the Ensembl website, supporting broad research use.