Discover Molecular Cloning Features

With CodonCode Aligner you can quickly and easily import and annotate sequences, create restriction maps, design primers, and simulate cloning experiments. CodonCode Aligner can also verify clones with automatic alignments and difference analyses, and create virtual gels.

This guide demonstrates some of the tools in CodonCode Aligner that will help make planning and executing your cloning experiments easier and faster.

Follow along as we go through a typical cloning workflow, importing files, choosing restriction enzymes, designing primers, the cloning simulation, verifying insert length and vector linearization, recording the cloning history, and clone validation.

Import Files

Import text and sequence files quickly and easily using drag & drop, with the import file menu, or directly from the source like Genbank.

View Sequences

After importing your files you can look at your sequences by viewing sequence maps or bases with customizable feature annotations and restriction enzyme cut sites.

Sequence Maps

To see the map for a sequence, open the base view ("View" menu ⇒ "Bases") and click on the Map button at the bottom. Maps are interactive and allow selection of features, sequence regions and enzymes. Customize the maps using the toolbar buttons on the left side.

Bases and Translations

For a detailed view look at the bases. Here, you can edit your sequence and see amino acid translations. Again the toolbar on the left side allows you to customize and show only features and enzymes that interest you.

Annotate Features

If you do have sequences without annotations, automatically annotate common features, transfer them between samples, or add your own.

Automatically identify functional elements that are commonly found in plasmids ("common features"), and add corresponding tags to the sequence using the Find Common Features... function from the "Sample" menu.
Transfer features from one sequence to another with the Transfer Tags option.
You can also add features manually by selecting the region you want to add the feature to, and selecting "Add Tag..." from the popup menu.

Restriction Enzymes

Customize which features and enzymes are displayed using the buttons in the toolbar on the left side of the base view, or in CodonCode Aligner's preference window. You can for example show only Genbank features, or make sure to display only enzymes that cut once in a sequence.

Save and load custom enzyme lists for enzymes you use often.

Simulate Cloning

Simulate different cloning workflows (like restriction cloning, TA cloning, Gibson Assembly, and more) in CodonCode Aligner. The cloning wizard for each technique guides you through all steps and helps resolve possible problems. Find the different cloning wizards in the "Tools" menu.

Primers and any other sequences that are part of your cloning process can be created as new samples or exported directly for ordering.

Learn more about virtual cloning in CodonCode Aligner on the molecular cloning site. For step-by-step instructions, watch the cloning videos on our tutorial page, or look at the how-to pages here in the learning center. For example, a guide for a HiFi DNA Assembly workflow can be found on the How-To: HiFi DNA Assembly page.

Virtual Gels

Use a gel to verify if your vector was linearized, or if the insert has the correct size after PCR. Simulate virtual gels by showing a restriction map with the enzyme(s) you want to use, and choose "Virtual Gel" in the restriction map options. There is an interactive selection that is synchronized across views, which highlights a fragment you select in the gel in other views like the base view.

To learn more about restriction maps and virtual gels, watch the restriction mapping video tutorial.

Cloning History

The cloning products you design in Aligner are fully annotated and come with a complete cloning history. That way you always have a record of exactly how the construct was created, making it easy to reproduce and share the cloning process.
The cloning history can be seen by selecting the History button at the bottom of the base view. Export and create primers directly from the cloning history.

Design Primers

Automatically design primers and see primer annotations.
When simulating cloning, primers can be generated automatically within the cloning process. But you can also design primers separately using the "Design Primers..." feature from the "Tools" menu. Design PCR or sequencing specific primers, for example after cloning to sequence and verify your insert.

Clone Verification

Once you have created your clones in the lab, CodonCode Aligner helps you validate the different clones. The clone verification tool automatically creates alignments to references, and shows a full report with results and difference analyses. The clone verification contains direct links to the created contig and trace files, allowing you to edit or see amino acid effects.

For a guide on clone verification, please look at the How-To: Verify Clones page.