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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.

Plasmids

Plasmids

Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...

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Related Experiment Video

Updated: Mar 17, 2026

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

Published on: February 5, 2021

plasmidSPAdes: assembling plasmids from whole genome sequencing data.

Dmitry Antipov¹, Nolan Hartwick², Max Shen³

¹Center for Algorithmic Biotechnology, Institute for Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia.

Bioinformatics (Oxford, England)

|July 29, 2016

Summary

This summary is machine-generated.

We developed plasmidSPAdes, a new software tool for assembling plasmids from whole genome sequencing data. This algorithm aids in extracting crucial plasmid-borne genes, such as those for antibiotic resistance, from bacterial genomes.

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Last Updated: Mar 17, 2026

Rapid Assembly of Multi-Gene Constructs using Modular Golden Gate Cloning

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Published on: February 5, 2021

Use of In Vivo Assembly for High-efficiency Plasmid Construction

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Published on: February 7, 2025

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

CAPRRESI: Chimera Assembly by Plasmid Recovery and Restriction Enzyme Site Insertion

Published on: June 25, 2017

Area of Science:

Genomics
Bioinformatics
Microbiology

Background:

Plasmids are extrachromosomal genetic elements crucial for bacterial adaptation and evolution.
They carry important genes, including those for virulence and antibiotic resistance.
Existing bioinformatics tools are insufficient for comprehensive plasmid data extraction from whole genome sequencing (WGS) projects.

Purpose of the Study:

To develop and evaluate a specialized software tool for plasmid assembly from WGS data.
To address the shortage of tools for analyzing plasmid-borne genes.

Main Methods:

Development of the plasmidSPAdes algorithm.
Benchmarking plasmidSPAdes performance on diverse bacterial genomes.

Main Results:

plasmidSPAdes effectively assembles plasmids from WGS data.
The tool demonstrates robust performance across various bacterial genomes.
Successful extraction of plasmid data, including important genes, is achieved.

Conclusions:

plasmidSPAdes is a valuable new tool for plasmid assembly and analysis.
It enhances the ability to study plasmid-borne genes from WGS data.
The software facilitates research in areas like antibiotic resistance and bacterial virulence.