Early Career Researcher Toolbox: Free Online Molecular Biology Tools

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.

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: Annotates features, BLASTs, aligns, digests, and translates a sequence.  
• NEBCutter2: For finding restriction enzyme cut sites
• Webcutter 2.0: For finding restriction enzyme cut sites
• Open reading frame finder 
• Addgene vector database: Find sequences for plasmids assembled from publications and commercially available sources, as well as those deposited with Addgene.
• NCBI BLAST: Compares nucleotide or protein sequences to sequences in a database
• ExPASy translation tool: Translates a DNA sequence using all six open reading frames
• UniProt: A database of protein sequence and functional information, such as expression patterns, post-translational modifications and polymorphisms
• Codon optimization tool: To access this tool, set up an IDT account.

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.

• Primer3 and Primer3Plus: For general primer design
• Design primers for Goldengate cloning  
• Design primers for In-Fusion Cloning
• Design primers for Gibson Assembly and NEB HiFi DNA Assembly 
• OligoAnalyzer Tool from IDT: For hairpin analysis, Tm and primer dimer estimation, and other primer characteristics.
• NEB Data-optimized Assembly Design (DAD): This tool designs overhang sets for high complexity Golden Gate Reactions
  
  

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. 

• NEB Ligation Calculator: This tool works for any cloning method. You can select from five different insert:backbone ratios.
• In-Fusion cloning molar ratio calculators

Lab math calculators

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

• Molarity calculator
• Promega's Biomath Calculators
• Primer resuspension calculator (sign-in required.) 
• DailyCalcs Science Calculator app for iPhone

Reagent and Data Repositories

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

• Addgene Data Hub: A data repository for validation data on Addgene/CLOVER viral vectors. 
• Caspedia: A data repository for Cas enzymes. 
• Open repository of CRISPR screens
• Cellosaurus: A knowledge resource for cell lines
• IBEX Knowledge Base: A data repository for validation data on IBEX reagents. 
• mAb3D atlas validated antibodies: A database of validated antibodies for mouse, human, and marmoset brain IHC. 
• FPbase: A data repository for fluorescent proteins and their properties. 
• Expasy: Bioinformatics resource portal which includes both bioinformatics tools and knowledge databases.

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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Additional resources on the Addgene blog:

• Learn how the CRISPR software matchmaker can help you choose the best CRISPR software for your needs
• 5 great apps for lab life 
• Sharing your lab protocols using apps to save you time and track your experiments 

Resources on Addgene.org:

• Read our Molecular Biology Reference
• Find molecular biology protocols
• Browse our protocol video collection