From rejected genes and truncated hits to verified production clones.
Repetitive structural proteins stall Twist, IDT, and GenScript synthesis and recombine out during host integration, while public database hits frequently arrive truncated at contig edges. We rebuild intact genes from raw reads, clear synthesis vendor screens without changing a single amino acid, and verify integrated clones on Nanopore or PacBio HiFi reads.
Clear vendor complexity rejections while preserving 100% protein identity.
Standard codon optimizers assign the highest-frequency codon to every repeat unit, creating exact DNA k-mers that fail Twist, IDT, and GenScript synthesis screens—and trigger homologous deletion in Pichia, Bacillus, or CHO. We globally minimize repeat k-mers, GC extremes, 5′ mRNA hairpins, and cryptic splice/poly-A motifs under a contingent guarantee: $0 if your vendor’s order-intake screen refuses the construct.
01 · You Provide
- Target amino-acid sequence (tandem-repeat collagen, silk, elastin, mucin/lubricin, solenoid, repeat binder, or CRISPR/TAL array).
- Chosen synthesis vendor, cloning overhangs / forbidden restriction sites, and expression host.
- Optional: multi-copy integration count if you need non-recombining sibling genes in one strain.
02 · Computational Protocol
- Repeat-free codon redesign: eliminates long direct and inverted DNA repeats across the entire gene while strictly locking 100% protein identity.
- Host expression tuning: enforces sliding-window GC bounds, 5′ ribosome-loading mRNA folding energy, and host cryptic splice / premature poly-A clearance across 17 bundled organisms (CHO, HEK293, Sf9, S. cerevisiae, P. pastoris, Y. lipolytica, A. niger, A. oryzae, T. reesei, E. coli, B. subtilis, B. licheniformis, B. megaterium, C. glutamicum, P. putida, L. lactis, V. natriegens, or custom hosts).
- Non-recombining multi-copy gene sets: optional diverged synonymous gene copies engineered below host homologous-recombination thresholds.
03 · Deliverable Package
- Order-ready FASTA/GenBank construct verified 100% identical in translated protein sequence.
- Before/after repeat-length, GC-window, 5′ mRNA ΔG, and restriction-site verification report.
- Related reading: Why codon optimizers fail vendor repeat screens →
| Package Tier | Scope & Contingent Guarantee | Turnaround | Fixed Fee | |
|---|---|---|---|---|
| Pre-Submission Vendor Screen Audit | Diagnostic complexity, repeat-window & host-splicing audit; credited 100% if you proceed to Full Rescue | 2 business days | $750 / construct | Select tier → |
| Full Synthesis-Rescue Redesign | Complete synonymous redesign + cloning cassette check; $0 deposit due at kickoff, invoiced only upon vendor acceptance | 3–5 business days | $4,000 / construct | Select tier → |
| Multi-Copy Non-Recombining Gene Set | Primary rescued construct + diverged synonymous gene copies for high-copy yeast, fungal, or bacterial integration | 4–5 business days | $4,000 + $1,500 / copy | Select tier → |
Reconstruct truncated database hits from raw reads before ordering dead DNA.
Public GenBank, JGI, and MGnify protein records routinely suffer from contig-edge truncations, collapsed repeat arrays, miscalled start codons, missed eukaryotic introns, omitted co-operon helper genes, or misattributed bacterial symbionts inside plant and marine assemblies. Ordering the raw accession wastes weeks of expression screening on a broken fragment.
01 · You Provide
- 1–10 public accessions (NCBI, UniProt, MGnify, JGI) or in-house draft contig sequences that under-express or appear truncated.
- SRA/ENA run identifiers or raw FASTQ files where available.
- Target heterologous expression host.
02 · Computational Protocol
- Rebuilding full-length genes from raw reads: recovers missing N/C-terminal ends, fixes assembly frameshifts, and resolves true repeat copy numbers.
- Intron, leader & operon check: corrects eukaryotic exon boundaries, identifies native secretion signals, and maps adjacent chaperones, maturation proteases, or cofactor enzymes.
- Source-organism & contamination check: separates genuine eukaryotic genes from bacterial symbiont or environmental contaminants so you choose the right expression host.
03 · Deliverable Package
- Healed full-length coding and mature amino-acid FASTAs + co-operon helper sequences.
- Before/after 3D PDB models demonstrating restored terminal caps and active-site closure.
- Taxonomic provenance & host-pathway recommendation memo.
| Package Tier | Locus & Operon Scope | Turnaround | Fixed Fee | |
|---|---|---|---|---|
| Focused Rescue | 1–3 database hits or draft contigs; locus extension, exon/frameshift healing, 3D cap check & operon/contaminant audit | 5 business days | $3,500 – $4,500 | Select tier → |
| Full Panel Rescue | 4–10 candidates including targeted SRA/ENA raw-read re-assembly and before/after 3D refolding | 5–7 business days | $5,000 – $7,500 | Select tier → |
Verify exact copy number, locus, and repeat integrity from ONT or HiFi reads.
Colony PCR and Sanger across junction primers miss off-target integrations, vector-backbone concatemers, disrupted host genes, and internal repeat-array deletions. Send raw Nanopore or PacBio HiFi whole-genome FASTQs (such as Plasmidsaurus microbial/yeast WGS) and receive a definitive per-clone banked-strain report.
01 · You Provide
- Raw Oxford Nanopore or PacBio HiFi FASTQ/BAM files for 1–12 engineered clones sharing a host reference.
- Intended donor plasmid/cassette GenBank or FASTA map.
- Parent host genome reference (or standard public reference strain).
02 · Computational Protocol
- Single-molecule spanning-read audit: directly measures cassette copy number and internal repeat length on uncollapsed reads without short-read assembly artifacts.
- Junction & off-target mapping: pinpoints every chromosomal insertion, plasmid backbone carry-over, inversion, and disrupted host ORF.
- Variant & mosaicism check: calls point mutations, indels, and sub-clonal deletion subpopulations inside the expression cassette.
03 · Deliverable Package
- Per-clone pass/fail master cell bank audit report (PDF/HTML + structured CSV).
- Phased junction alignments, copy-number histograms, and IGV-ready BAM/VCF tracks.
- Related reading: Short-read assemblers collapse tandem repeats →
| Package Tier | Clone Cohort Size | Turnaround | Fixed Fee | |
|---|---|---|---|---|
| Base Cohort | 1 to 4 clones on the same host genome & construct series | 5 business days | $2,500 flat | Select tier → |
| Expanded Cohort | 5 to 8 clones on the same host reference (+$500 per clone above 4) | 5–6 business days | $3,000 – $4,500 | Select tier → |
| Plate Cohort | 9 to 12 clones on the same host reference (+$500 per clone above 4) | 6–8 business days | $5,000 – $6,500 | Select tier → |
Continue across the computational R&D lifecycle.
Protein Triage & Sequence Optimization
300 K / 330 K explicit-solvent MD triage and active-site-locked sequence liability scrubbing.
Assay Video, Melting Curves & Plate Kinetics
Automated curves and figures from DSF melt exports, clearing and fluorescence time-lapses, thermal-camera plates, and 96-well freezing runs.
Patent-Clear Discovery & Sequence Audits
Low-identity 3D homolog & ASR panels, pre-filing claim & ST.26 audits, and SPPS miniprotein discovery.