In-Fusion cloning molar ratio calculator. You can select from five different insert:backbone ratios. NEB Ligation Calculator: This tool works for any cloning method. 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. OligoAnalyzer Tool from IDT: For hairpin analysis, Tm and primer dimer estimation, and other primer characteristics. Design primers for Gibson Assembly and NEB HiFi DNA Assembly. Primer3 and Primer3Plus: For general primer design. 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. 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. 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. Sometimes DNA sequences need to be “cleaned up” or changed in some way before you can analyze them. Codon optimization tool: To access this tool, set up an IDT account.įigure 2: Addgene's Analyze Sequence tool. 
UniProt: A database of protein sequence and functional information, such as expression patterns, post-translational modifications and polymorphisms.ExPASy translation tool: Translates a DNA sequence using all six open reading frames.NCBI BLAST: Compares nucleotide or protein sequences to sequences in a database.Addgene vector database: Find sequences for plasmids assembled from publications and commercially available sources, as well as those deposited with Addgene.Webcutter 2.0: For finding restriction enzyme cut sites.NEBCutter2: For finding restriction enzyme cut sites.
Addgene's analyze sequence tool: Annotates features, BLASTs, aligns, digests, and translates a sequence. Wayne Davis from the University of Utah.įigure 1: A plasmid map created in SnapGene of Blue Flame plasmid pET21a-BirA.ĭNA / protein database search and analysis tools ApE (A plasmid Editor): A free, donation-based plasmid analysis tool including editing, annotating, creating maps, and more. SNAPGENE FREE ALTERNATIVE SERIAL
Serial Cloner: Free desktop-based software for plasmid design and mapping.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.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).These tools are for viewing, editing or making plasmid maps, but can also analyze and annotate any DNA sequence. 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.
We all have our favorite tools for tackling these particular tasks, but they tend to be scattered about the internet.
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