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Plasmodesmata

Plasmodesmata

The organs in a multicellular organism’s body are made up of tissues formed by cells. To work together cohesively, cells must communicate. One way that cells communicate is through direct contact with other cells. The points of contact that connect adjacent cells are called intercellular junctions.

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: Aug 1, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

PlasMapper 3.0-a web server for generating, editing, annotating and visualizing publication quality plasmid maps.

David S Wishart^1,2,3,4, Leah Ren¹, Jacques Leong-Sit¹

¹Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada.

Nucleic Acids Research

|April 26, 2023

Summary

This summary is machine-generated.

PlasMapper 3.0 is a powerful web server for creating, editing, and visualizing plasmid maps, essential tools for gene cloning experiments. This updated version offers advanced features for plasmid annotation and design, improving research efficiency.

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Last Updated: Aug 1, 2025

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

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Area of Science:

Molecular Biology
Bioinformatics
Synthetic Biology

Background:

Plasmid maps are crucial for documenting and communicating gene cloning experiments.
Existing tools may lack comprehensive features or user-friendly interfaces for plasmid design and visualization.
PlasMapper 2.0 provided foundational plasmid mapping capabilities.

Purpose of the Study:

To introduce PlasMapper 3.0, an enhanced web server for generating, editing, annotating, and visualizing publication-quality plasmid maps.
To offer advanced functionalities comparable to commercial software for plasmid manipulation.
To improve the user experience and graphical output for plasmid data representation.

Main Methods:

Users can input plasmid sequences via pasting or uploading, or select from a database of over 2000 pre-annotated plasmids (PlasMapDB).
PlasMapper 3.0 utilizes an internal feature database for annotating novel plasmids with common genetic elements.
Interactive tools allow for sequence editing, feature modification, and codon optimization.

Main Results:

PlasMapper 3.0 provides an upgraded, interactive, full-color plasmid viewer/editor with enhanced graphical capabilities.
The server supports comprehensive annotation of existing and new plasmids.
Users can download plasmid maps and associated data in multiple formats.

Conclusions:

PlasMapper 3.0 significantly enhances the process of plasmid map generation, editing, and visualization.
The tool offers advanced features for researchers involved in gene cloning and synthetic biology.
It serves as a valuable, accessible resource for planning, designing, and publishing molecular biology experiments.