RayCrest Molecular Design Studio

PLASMID EDITOR + PRIMER DESIGN

Plasmid editor and primer design workspace for Mac

Edit constructs in sequence and map context, design primers, plan in silico PCR checks, and stage digest or cloning simulation — all without leaving the construct you're actually working on.

MDS Sequence Workspace with protein overlay and selection context

OUTCOMES

What teams get from one plasmid editor and plasmid map maker

Edit with sequence and map context

Move between sequence-level editing and publication-ready plasmid map output without rebuilding the construct in separate plasmid map software.

Design primers and plan in silico PCR in place

Primer workflows stay attached to the exact region, construct, and annotation context under review.

Know your digest will work before you cut

Preview fragments and virtual gel expectations before you set up the reaction.

Simulate your assembly before ordering anything

Stage Gibson or restriction workflows while mistakes are still cheap to catch.

FEATURE WALKTHROUGH

How RayCrest handles plasmid editing and primer workflows

Circular plasmid map linked to the construct under edit

Sequence and map views stay tied to the same construct

Use RayCrest as a plasmid editor and plasmid map maker without losing the underlying sequence context that makes the construct interpretable.

  • Switch between sequence review and map communication without rebuilding annotations.
  • Feature labels, ORFs, restriction sites, proteins, and primers stay linked to the construct.
  • Edits remain grounded in the same construct history used for downstream validation and export.
Primer Wizard with design modes and constraints

Primer Wizard plus in silico PCR planning

Highlight a region of your construct and design primers right there, with in silico PCR-oriented planning kept in the same construct-aware workflow.

  • Single, qPCR, cloning, and QuikChange-style mutagenesis modes.
  • Live controls for length, Tm, GC%, and GC clamp behavior.
  • Primer design stays connected to the region, annotations, and downstream cloning plan.
Digest planner with enzyme selection, fragment table, and virtual gel

Digest planning plus virtual gel

Choose enzymes with clearer fragment-level expectations before cutting DNA or sending a plan to a teammate.

  • Single and combined digest modes.
  • Fragment tables with coordinates and sequence context.
  • CSV-ready fragment export for downstream planning.
Cloning wizard showing staged inserts and Gibson simulation controls

Cloning simulation before commit

Simulate your entire cloning plan before you touch a pipette. Check overlaps, review fragment order, and export a shareable report before you have ordered a single primer.

  • Technique recommendation with confidence hinting
  • Overlap sizing and Tm controls for practical tuning
  • Simulation output that can be shared as PDF

TECHNICAL DETAILS

Advanced controls, overlays, and import compatibility

Primer design software modes, constraints, and 5′ adapter support

Lower-level primer controls remain available without forcing a separate tools workflow or a detached export/import loop.

  • Design modes cover single primers, qPCR, cloning, and QuikChange-style mutagenesis.
  • Constraint tuning includes primer length, Tm, GC%, and guardrails such as GC clamp preferences.
  • Add 5′ tail sequences for restriction cloning, Golden Gate, Gibson Assembly, or any custom adapter. The wizard appends them automatically.
  • In silico PCR software and primer design live in the same construct-aware workspace, alongside digest and cloning decisions.
Sequence annotations, ORF and restriction overlays, and map context

When you are editing a construct, MDS keeps sequence annotations and coding context visible so map making and bench planning stay grounded in the same source sequence.

Sequence view with protein overlay and linked selection context
Tooltip showing amino-acid and codon indexing
  • Sequence annotations, ORFs, restriction sites, proteins, and primers remain linked through edits.
  • Selection interactions expose codon and amino-acid indexing for faster review in coding regions.
  • The same coding-region context keeps codon optimization and reverse translate close to downstream construct edits.
  • Map and sequence views stay anchored to the same construct rather than drifting across separate files.
Import and interoperability for construct editing

Open GenBank, FASTA, and SnapGene .dna files in the same plasmid editing workflow.

  • Import verified formats including GenBank, FASTA, and SnapGene .dna files.
  • Use the imported construct as the same source for primer design, digest analysis, and cloning simulation.
  • Move from editing to validation with direct links to Sanger and FASTQ review workflows.

WORKFLOW + OUTPUTS

From imported construct to cloning handoff

Typical workflow

  1. Open

    Open a GenBank file, FASTA file, or SnapGene .dna file and your features, overlays, and construct context are ready for editing.

  2. Plan

    Edit the plasmid, design primers, run in silico PCR and digest checks, and stage your Gibson or restriction workflow from the same construct.

  3. Share

    Export order-ready primer sequences, a fragment CSV, and a PDF cloning report in one step.

Outputs

  • Updated construct record with annotations and overlays preserved
  • Order-ready primer sequences with optional 5′ adapters
  • Digest fragment sets with optional CSV export and virtual gel preview
  • Cloning simulation report for notebooks and collaborator review

RELATED NEXT STEPS

Keep the construct moving

Primer Design

Go deeper on primer design and in silico PCR

See the dedicated workflow page for Primer Wizard positioning, primer modes, and construct-aware planning.

Primer design workflow

Protein Design

Keep codon optimization and reverse translate near construct edits

Use the dedicated page when protein-to-DNA design work needs to stay close to the plasmid, primers, and map context.

Codon optimization workflow

Validation

Check Sanger traces and mismatches after the build

Move from plasmid editing into AB1, chromatogram, and FASTQ-backed validation without losing construct history.

AB1 and validation workflow

Interoperability

Bring in SnapGene .dna files and keep working locally

See the verified compatibility story for SnapGene import, GenBank, FASTA, Sanger, and FASTQ inputs.

SnapGene alternative details

Figures

Turn the edited construct into a shareable map

Move from plasmid editing into figure-ready circular, linear, and rectangular outputs without rebuilding the construct elsewhere.

Presentation figures

Edit, design primers, and simulate cloning from one Mac workspace

Beta access is free. We review every request within 24 hours.

Request Beta Access See Presentation Figures