Sequence assembly
5 methods · 2016–2026
Sequence assembly: Sequencing a whole protein rather than a peptide. Overlapping peptides are called first, then assembled into full-length sequence, which is how antibodies and protein therapeutics are sequenced without a reference.
Sequencing a whole protein rather than a peptide. Overlapping peptides are called first, then assembled into full-length sequence, which is how antibodies and protein therapeutics are sequenced without a reference.
The earliest of its 5 methods is ALPS (2016); 4 more have followed.
| Methods | 5 |
| Papers describing them | 6 |
| Authors | 36 |
| Active | 2016-08-26 to 2026-08-13 |
| Kinds | post-processor (5) |
| Acquisition | DDA (4) |
Methods (5)
Oldest first, by the paper that describes each one.
- ALPS (2016): Assembles de novo sequenced peptides and their per-residue confidence scores into a de Bruijn graph to reconstruct complete monoclonal antibody heavy and light chains without a template.
- Stitch (2024): Assembles de novo peptides from Casanovo, PEAKS, pNovo and MaxNovo into full antibody sequences, and corrects the two error classes that assembly alone cannot: mass coincidences, where a different residue combination matches the same mass, and I/L ambiguity.
- InstaNexus (2025): End-to-end workflow for reference-free sequencing of full-length protein therapeutics. Multi-protease digestion yields overlapping peptides, InstaNovo sequences them de novo and Winnow rescores, then greedy overlap or de Bruijn graph assembly (default k=7, min overlap 3) reconstructs contigs ranked by a composite score over coverage, N50, scaffold count and identity. Validated on nanobodies, monoclonal antibodies and de novo mini-binders.
- SequenceAssembler (2025): Post-identification tool that assembles full-length protein sequences by unifying peptide-spectrum matching (PSM) and de novo sequencing outputs from Novor Cloud, PEAKS Studio, and PatternLab for Proteomics; one-click GUI and comparable in performance to Stitch.
- borgonovo (2026): Reference-free protein sequencer: multi-protease digestion tiles a protein with overlapping peptides, and the redundant de novo reads are assembled into a per-residue consensus by substitution-tolerant alignment and per-column voting. Re-decoding each spectrum under a prior from its consensus position raises amino-acid accuracy. Wraps Casanovo by default but is backend-agnostic.
Papers describing them (6)
- Complete De Novo Assembly of Monoclonal Antibody Sequences (2016, Scientific Reports, peer-reviewed)
- A Handle on Mass Coincidence Errors in De Novo Sequencing of Antibodies by Bottom-up Proteomics (2024, Journal of Proteome Research, peer-reviewed)
- Generalizable direct protein sequencing with InstaNexus (2025, bioRxiv, preprint)
- SequenceAssembler: A tool for protein sequence assembly from mass spectrometry data (2025, Journal of Proteomics, peer-reviewed)
- Generalizable Direct Protein Sequencing With InstaNexus (2026, Molecular & Cellular Proteomics, peer-reviewed)
- Reference-free protein sequencing by consensus assembly of redundant de novo peptide reads (2026, bioRxiv, preprint)