Built by bench scientists

Design plasmids. Validate the evidence. Share clean constructs.

RayCrest MDS brings plasmid editing, primer design, Sanger and FASTQ-backed validation, protein context, cloning simulation, and polished map export into one local-first Mac workspace.

Download on the Mac App Store Free manual primer design · Pro automation available
RayCrest plasmid map editor with layer controls and export options
RayCrest sequence workspace showing base-level editing with protein annotations
RayCrest Sanger evidence view showing chromatogram peaks near a mismatch
Live sequence editing Polished plasmid maps Evidence at the peak Coding-impact calls

Opens natively

GenBank · .gb / .gbk FASTA SnapGene · .dna Sanger · .ab1 / .abi FASTQ GFF3 EMBL

A construct’s journey

One construct. Every step connected.

Follow the same construct from base-level editing to primer design, sequencing review, and final map export. Every view stays connected, and your construct never leaves your Mac.

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Step 01 · Edit

Edit with sequence context in view.

Open a construct and edit at single-base resolution while codons, amino acids, ORFs, features, and restriction sites update around the active selection.

  • Codon and amino-acid overlays update live
  • Features and restriction sites stay visible
  • Selections carry into primers, QC, maps, and protein views
RayCrest sequence workspace with codon, protein, and restriction overlays

Step 02 · Design

Design primers from the active region.

Create sequencing, qPCR, cloning, and QuikChange primers from the same selection, with Tm targets, hairpin warnings, and primer-library matches in view.

  • 5′ tails and exact-edge anchors
  • Primer-library matches pre-checked
  • Ranked candidates with diagnostic flags
RayCrest Primer Wizard showing cloning primer candidates and primer-library hits

Step 03 · Validate

Resolve mismatches from real evidence.

Review AB1 chromatograms and FASTQ-backed reads while each flagged base stays linked to the construct, consensus call, and coding-impact panel.

  • Chromatogram peak at the selected mismatch
  • Protein-impact call available on demand
  • QC decisions saved with the evidence
RayCrest Sanger evidence view showing chromatogram peaks near a mismatch

Step 04 · Publish

Export a figure-ready plasmid map.

Generate circular, linear, or rectangular maps from the reviewed construct. Pin labels, control tracks, focus regions, and export to image, vector, or PowerPoint.

  • Layer browser for figure-ready styling
  • Region focus for cropped figures
  • Image, vector, and PPT export
RayCrest plasmid map editor with layer controls and export options
RayCrest sequence workspace with codon, protein, and restriction overlays Codon + protein overlay Active selection

Connected product surfaces

Design work, evidence review, protein context, and figure-ready output stay connected.

RayCrest’s views share the same construct, so edits, primer choices, validation evidence, protein annotations, and exported figures stay in sync.

Sequence workspace

Edit, annotate, and analyze from the active sequence.

Base-level editing with codon, amino-acid, ORF, feature, and restriction overlays. Launch primer, digest, cloning, QC, and protein tools without losing your selection.

RayCrest sequence workspace with codon, protein, and restriction overlays Protein overlay Active selection

Alignments + QC

Make every mismatch decision from the evidence.

Review Sanger AB1 chromatograms and FASTQ-backed reads in one QC surface. Jump from a flagged base to the peak, consensus call, and coding impact.

RayCrest alignments and QC view with automated mismatch detection Mismatch detection Coding-impact panel

Primer wizard

Design sequencing, qPCR, cloning, and mutagenesis primers.

Generate ranked candidates with Tm targets, 5′ tails, exact-edge anchors, hairpin warnings, and primer-library matches.

RayCrest Primer Wizard showing cloning primer candidates and primer-library hits Cloning mode Primer-library hits

Presentation figures

Create polished plasmid maps from reviewed constructs.

Circular, linear, and rectangular maps share your construct annotations. Pin labels, choose tracks, focus regions, and export to image, vector, or PowerPoint.

RayCrest plasmid map editor with layer controls and export options Layer browser Image & PPT export

Protein + structure

See sequence changes in protein and structure context.

Move from coding sequence to amino-acid annotations, protein alignments, and 3D structure views without losing the selected region.

  • Sync selections between plasmid, protein, and 3D structure views
  • Review protein MSAs and UniProt-linked annotations
  • Style amino-acid glyphs for review, talks, and handoffs
  • Focus selected residues in the 3D structure view
RayCrest amino acid glyph style preview Amino-acid glyph styles
Plasmid view
RayCrest plasmid view with linked coding sequence and amino acid track
Protein view
RayCrest protein sequence view with multiple sequence alignment annotations
Structure view
RayCrest protein structure view with selected residue context

In silico cloning

Plan Gibson, Golden Gate, restriction, In‑Fusion, and Gateway assemblies in silico.

Stage backbones and inserts, simulate every junction, verify overlaps and orientation, and only create the construct when every check passes.

  • Auto-sized overlaps with explicit Tm targets
  • Junction diagnostics tied to each staged part
  • Bench-ready recipe with reaction size and polymerase preset
RayCrest Cloning Designer with staged backbone, insert, assembly schematic, and diagnostic junction report
Simulate before ordering Junction diagnostic

8 workflows

Sequence editing, primer design, cloning simulation, digest planning, Sanger/FASTQ QC, protein MSA, structure view, and map export — connected.

100% local

Your constructs and reads stay on your Mac. Nothing uploaded.

7 formats

GenBank, FASTA, SnapGene .dna, AB1/ABI, FASTQ, GFF3, and EMBL.

macOS 13+

macOS Ventura or later. Apple Silicon and Intel.

Stop switching tools for construct work.

Start free with manual primer design, native file import, plasmid editing, and evidence review. Add Pro for Primer Wizard automation, Sanger/FASTQ QC decisions, cloning simulation, protein/structure tools, and publication-ready map export.

Download on the Mac App Store See Pro pricing