Early Career Researcher Toolbox: Free Online Molecular Biology Tools

By Beth Kenkel

Primer design. Plasmid mapping. DNA sequence analysis. We all have our favorite tools for tackling these particular tasks, but they tend to be scattered about the internet. To help you keep your virtual molecular biology toolbox organized, today’s post features a list of free online molecular biology tools all in one place.

Plasmid mapping

These tools are for viewing, editing or making plasmid maps, but can also analyze and annotate any DNA sequence.

  • SnapGene Viewer: The free SnapGene Viewer is great for looking at plasmid maps and viewing sequencing traces, while the paid version provides more tools for plasmid mapping and design (Figure 1).
  • Benchling: While you might think of Benchling as an electronic lab notebook, it also has a suite of molecular biology tools and can make plasmid maps. Free for academic users.
  • Serial Cloner: Free desktop-based software for plasmid design and mapping.
  • ApE (A plasmid Editor): A free, donation-based plasmid analysis tool including editing, annotating, creating maps, and more. This tool is maintained by M. Wayne Davis from the University of Utah.


Plasmid map. Annotations on the outside of the plasmid indicate cut sites; annotations on the inside of the plasmid indicate parts of the plasmid.
Figure 1: A plasmid map created in SnapGene of Blue Flame plasmid pET21a-BirA.


DNA / protein database search and analysis tools

Addgene's analyze sequence tool shows the DNA sequence and options for BLAST, align, digest, and translate the sequence
Figure 2: Addgene's Analyze Sequence tool.


DNA sequence manipulation tools 

Sometimes DNA sequences need to be “cleaned up” or changed in some way before you can analyze them. These tools help with that. 

  • DNA sequence reverse complement tool: Enter a DNA sequence and the program will give you the reverse sequence, complement sequence, or reverse and complement sequence. 
  • Filter DNA tool: Removes non-DNA characters, such as numbers and blank spaces, from the text of a DNA sequence, making it ready to copy and paste into other applications

Primer design tools

Many of the above-listed plasmid mapping tools have built-in primer design tools, but here are a few stand-alone sites for general primer design, as well as primer design for different cloning applications.

Cloning ligation reaction calculators

These links can help you calculate how much insert and backbone you need for different types of cloning methods, such as restriction enzyme cloning, Gibson assembly, or In-Fusion cloning. 

Lab math calculators

These calculators can help you with common calculations performed in the lab.

Reagent and Data Repositories

These links can help you find experimental and/or validation data on molecular biology tools. 

Do you have a favorite online molecular biology tools not listed in today’s post? Share them in the comments below.

This post was written in April 2020 by Beth Kenkel. Additional resources were added in September 2023 by Rachel Leeson. 

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Resources on Addgene.org:

Topics: Plasmid Cloning, Plasmids, Early Career Researcher

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