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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.

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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: Nov 4, 2025

Protein Engineering by Yeast Surface Display

Protein Engineering by Yeast Surface Display

Published on: November 29, 2024

pLannotate: engineered plasmid annotation.

Matthew J McGuffie¹, Jeffrey E Barrick¹

¹Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, 2500 Speedway A5000, Austin, TX 78712, USA.

Nucleic Acids Research

|May 21, 2021

Summary

This summary is machine-generated.

Researchers developed pLannotate, an open-source web server for comprehensive plasmid annotation. This tool addresses incomplete functional element information in engineered plasmids, improving experimental reliability and data accuracy in biological sciences.

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Area of Science:

Molecular Biology
Bioinformatics
Synthetic Biology

Background:

Engineered plasmids are crucial tools in biological research, but their functional annotation is often incomplete due to reused and remixed DNA sequences.
Incomplete or inaccurate plasmid feature information can lead to experimental failures and unintended consequences.
Existing annotation tools lack comprehensive feature libraries and fail to detect fragmented or novel sequences common in engineered plasmids.

Purpose of the Study:

To develop an open-source web server, pLannotate, for rapid and thorough annotation of engineered plasmid features.
To provide researchers with a tool that overcomes the limitations of existing plasmid annotation methods.

Main Methods:

Developed the pLannotate web server, utilizing extensive databases of genetic parts and proteins.
Implemented a filtering algorithm to identify and display the most relevant feature matches, including feature fragments.
Integrated visualization of annotated plasmid maps, feature provenance explanation, and downloadable results in multiple formats.

Main Results:

pLannotate provides comprehensive annotation of engineered plasmid features, including novel and fragmented sequences.
The tool accurately identifies and reports the presence, location, and identity of plasmid elements.
Users can visualize annotated plasmids, understand the origin of predictions, and export data easily.

Conclusions:

pLannotate significantly enhances the annotation of engineered plasmids, improving experimental design and reproducibility.
The open-source nature and comprehensive features of pLannotate make it a valuable resource for the biological sciences community.
Accurate plasmid annotation is essential for advancing research in molecular biology, bioinformatics, and synthetic biology.