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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-wide Association Studies-GWAS

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...

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...

Genome Size and the Evolution of New Genes

Genome Size and the Evolution of New Genes

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.

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Related Experiment Video

Updated: Mar 30, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Assembly: a resource for assembled genomes at NCBI.

Paul A Kitts¹, Deanna M Church², Françoise Thibaud-Nissen²

¹National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA kitts@ncbi.nlm.nih.gov.

Nucleic Acids Research

|November 19, 2015

Summary

The NCBI Assembly database offers stable tracking for diverse genome assembly data, from simple bacterial chromosomes to complex human genomes. It provides unique accessions and detailed metadata for efficient genome data management and retrieval.

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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Related Experiment Videos

Last Updated: Mar 30, 2026

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Hybrid De Novo Genome Assembly for the Generation of Complete Genomes of Urinary Bacteria using Short- and Long-read Sequencing Technologies

Published on: August 20, 2021

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

Published on: August 15, 2019

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Area of Science:

Genomics
Bioinformatics
Data Management

Background:

Genome assembly data requires robust tracking and standardization.
Diverse genome structures necessitate a flexible data model.
Accurate metadata is crucial for genomic research.

Purpose of the Study:

To introduce the NCBI Assembly database as a resource for genome assembly data.
To highlight the database's capabilities in accommodating various assembly structures.
To detail the accessioning, tracking, and reporting functionalities for genome assemblies.

Main Methods:

Development of a database model to support diverse genome assembly structures.
Implementation of a stable accessioning system for genome assemblies.
Integration of metadata reporting, including statistical reports and update history.
Tracking relationships between INSDC submissions and NCBI RefSeq assemblies.

Main Results:

The NCBI Assembly database provides stable accessions and versioning for genome assemblies.
It accommodates a wide range of assembly complexities, including bacterial and human genomes.
The database offers comprehensive metadata, statistical reports, and update tracking.
Users can easily query, browse, and download genome assembly data.

Conclusions:

The NCBI Assembly database is a vital resource for managing and accessing genome assembly data.
Its flexible model and comprehensive features support diverse genomic research needs.
The database enhances data discoverability and usability for the scientific community.