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Comprehensive, user-friendly design tools for DNA, protein sequences, and oligonucleotides

Build, share, and record DNA, RNA, and amino acid sequences in one unified platform.
Molecular biology software

The first complete molecular biology suite built within a platform

  • 10+ tools in one collaborative environment

    Track all of your sequence edits through a complete version history. Work together with shared libraries to eliminate duplicate efforts.

  • End-to-end traceability

    See the downstream samples and results that any sequence has led to. For example, see the binding affinity of all antibody lots with a given light chain variable fragment.

  • Unified sequence design and registration

    Design and register sequences in the same interface. In Requests and Workflows, specify registered sequences to be used in fulfillment.

DNA sequence software for molecular biology

More than 10 cutting-edge tools in one

  • Alignments and multi-sequence alignments. Learn more about Alignments
  • Translate directly from DNA sequences to amino acid sequences
  • Digest & ligate, gibson, and golden gate assembly
  • Automatic sequence annotation with shared annotation libraries
  • Automatically compute biochemical properties for any sequence
  • Annotate amino acid sequences with antibody-specific information, including CDRs and framework regions Learn more about Antibody Property Prediction Tools
  • Design, analyze, and develop RNA therapeutics within Benchling. Standardize oligonucleotide representation using HELM
CRISPR sequence analysis tools


  • Design guides with on-/off-target scoring
  • Share a gRNA repository with your organization
  • Design your own HDR templates
  • Access more than 100 genomes
Bulk assembly software for molecular biology

Bulk tools

  • Bulk assembly (digest & ligate, gibson, and golden gate)
  • Bulk DNA to amino acid translation
  • Bulk gene import from genomes
  • Bulk CRISPR guide design with on-/off-target scoring
Benchling registry

Unified Registry

  • Register DNA, RNA, and AA sequences directly from Molecular Biology. Those sequences can then be used and referenced across all Benchling applications
  • Upon registering a DNA, RNA, or AA sequence, the Registry automatically extracts sequence properties as data fields on the newly registered sequence
  • Upon registering a DNA or RNA construct, the Registry automatically detects, registers, and interlinks the construct’s components
  • Structure uniqueness constraints to ensure that no duplicate sequences are registered

“The molecular biology module has been really helpful for us, because it's actually accessible to the entire organization. Within discovery we can design a new construct, and when manufacturing has to produce it for a clinical candidate, they can just go into Benchling and find that exact DNA sequence.”

Tiffany Chen
Director of Discovery

Learn More about Molecular Biology

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