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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.

Genomic DNA in Prokaryotes

Genomic DNA in Prokaryotes

The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
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Prokaryotic Gene Structure and Organization

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...

Prokaryotic cells

Prokaryotic cells

Prokaryotes are small unicellular organisms that include the domains—Archaea and Bacteria. Bacteria include many common organisms, such as Salmonella and E. coli, while the Archaea include extremophiles that live in harsh environments, such as volcanic springs.Like eukaryotic cells, all prokaryotic cells are surrounded by a plasma membrane, have genetic material in the form of single, circular DNA, a cytoplasm that fills the interior of the cell, and ribosomes that synthesize proteins. However,...

Prokaryotic Cells

Prokaryotic Cells

Prokaryotes are small unicellular organisms that include the domains — Archaea and Bacteria. Bacteria include many common microorganisms, such as Salmonella and E. coli, while the Archaea include extremophiles that live in harsh environments, such as volcanic springs.
Like eukaryotic cells, all prokaryotic cells are surrounded by a plasma membrane, have genetic material in the form of single, circular DNA, a cytoplasm that fills the interior of the cell, and ribosomes that synthesize proteins.

Prokaryotic Cells

Prokaryotic Cells

Prokaryotes are small unicellular organisms that include the domains—Archaea and Bacteria. Bacteria include many common organisms, such as Salmonella and E. coli, while the Archaea include extremophiles that live in harsh environments, such as volcanic springs.Like eukaryotic cells, all prokaryotic cells are surrounded by a plasma membrane, have genetic material in the form of single, circular DNA, a cytoplasm that fills the interior of the cell, and ribosomes that synthesize proteins. However,...

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Updated: Jun 15, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

An Ergatis-based prokaryotic genome annotation web server.

Chris Hemmerich¹, Aaron Buechlein, Ram Podicheti

¹Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA.

Bioinformatics (Oxford, England)

|March 3, 2010

Summary

This summary is machine-generated.

Integrative Services for Genomics Analysis (ISGA) simplifies complex bioinformatics pipelines for prokaryotic genome annotation. This web-based server empowers biologists to customize and run analyses, overcoming the limitations of the complex Ergatis system.

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Published on: August 20, 2021

Area of Science:

Bioinformatics
Genomics
Computational Biology

Background:

Ergatis is a flexible but complex workflow management system for bioinformatics pipelines.
Its complexity limits its use to highly skilled bioinformaticians.
Biologists often require accessible tools for genome annotation.

Purpose of the Study:

To develop a user-friendly web-based server for prokaryotic genome annotation.
To build upon the Ergatis system, integrating additional analysis tools.
To provide intuitive interfaces for biologists to customize and execute annotation pipelines.

Main Methods:

Development of a web-based server named Integrative Services for Genomics Analysis (ISGA).
Integration of the Ergatis workflow system with other dynamic analysis tools.
Design of intuitive web interfaces for user customization and pipeline execution.

Main Results:

ISGA provides an accessible platform for prokaryotic genome annotation.
The system allows biologists to customize and execute their own annotation pipelines.
ISGA is designed for installation at genomics core facilities.

Conclusions:

ISGA simplifies complex bioinformatics workflows for genome annotation.
The server enhances accessibility for biologists, reducing reliance on specialized bioinformaticians.
ISGA facilitates custom prokaryotic genome analysis through an intuitive web interface.