Introduction
Bio-sequence searching is a critical process that identifies relevant prior art and competitive disclosures when novelty and scope of protection are based on the exact order of nucleotides or amino acids, rather than traditional keyword searching. This specialized approach is essential for securing and defending intellectual property (IP) rights.
TT Consultants conducts bio-sequence searches in support of novelty and scope of protection for diagnostic, therapeutic, and platform inventions. Our methodology utilizes a powerful combination of bioinformatics-driven alignment searches, targeted keyword restrictions, and patent-specific databases to ensure comprehensive coverage.
TT Consultants supports a wide range of sequence search types, including:
- Amino acid & Nucleic Acid Sequence Search
- Full-length sequence searches (proteins/polypeptides; antibody heavy/light chains etc.)
- Short sequence searches (motifs, epitopes, CDRs, fragments)
- Markush-style / variable-position searches and variant mapping
- Homology, identity, similarity analysis with local and global alignment
- Sequence & chemical compound conjugate search
Bioinformatics Know-How: Our Key Differentiators
Our search quality is driven by the expertise of our molecular biologists and bioinformaticians, ensuring our results go far beyond default search engine runs.
- Expert Tuning: Our searches are tuned by experts, not just relying on default BLAST runs.
- Degeneracy Consideration: We account for degeneracy in nucleic-acid searches, including silent mutations and non-coding complexity.
- Low-Complexity Masking: We mask low-complexity regions (e.g., poly-A tails, CA repeats, proline-rich regions) to prevent spurious, non-meaningful hits.
- Statistical Significance: We use E-values to interpret statistical significance, understanding that larger databases can artificially inflate hit counts and reduce the true significance of a match.
Our approach to scoring matrices and gap penalties is tailored to the specific sequence being analyzed:
| Sequence Type | Scoring Matrix/Strategy | Purpose |
|---|---|---|
|
Longer or Divergent Protein |
BLOSUM62 |
Offers a balanced trade-off between sensitivity and specificity. |
|
Shorter or Highly Similar Protein |
PAM30 or BLOSUM80 |
Used to improve sensitivity for close homology. |
|
Closest Relatives |
Strict Gap Penalty |
Intended for high-precision results. |
|
Divergent Relatives |
Permissive Gap Penalty |
Used for high-recall results. |
The Art of Claim Interpretation in Sequence Search
“A fundamental prerequisite for carrying out an excellent biological sequence search is accurate interpretation of the claim language.”
The scope of the sequence, identity or similarity thresholds, functional constraints, and allowed variants or positional flexibility must be thoroughly examined.
Key Claim Types and Evaluation
- Percent Identity Claims (e.g., “at least 95% identical to SEQ ID NO:1”): Must be evaluated to determine the correct denominator (query vs. subject sequence), whether the alignment coverage satisfies the claim, and if the claim is directed to the full-length sequence or only a defined segment.
- Percent Similarity Claims (e.g., “at least 80% similar to residues 34–210”): Requires assessment of the treatment of conservative amino acid substitutions and the specific scoring matrix or similarity algorithm used.
- Markush or Alternative Residue Claims (e.g., Zaa-Pro-Yaa-Ser, where Zaa and Yaa represent defined residue groups): These are modeled as a motif or variant sequence space, accounting for all permitted residue combinations.
- Variation-Position Claims (e.g., substitutions at explicitly defined positions): Evaluated on a position-by-position basis to determine whether identified variants fall within the claimed scope.
- Antibody Drug Conjugate (ADC) Related Claims: These require separate and collective analysis of three components:
- The antibody component (e.g., variable region sequences, CDR definitions, percent identity/similarity).
- The conjugation site(s) and linker chemistry (site-specific vs. stochastic conjugation, permissible attachment residues).
- The drug payload or functional limitation (e.g., cytotoxic activity or mechanism).
Comprehensive Deliverables for Your IP Strategy
Our reports are designed to be immediately useful for your legal and R&D teams, providing clear, claim-mapped evidence.
The closest-hit set contains the following essential data points:
- Alignment coverage
- Identity/similarity scores
- E-value significance
In addition, our reports include:
- Family-level patent mapping (priority, assignee, jurisdictions) for key hits.
- Claim-mapped relevance notes (the reason why a hit reads with respect to identity/similarity/variant language).
Optional deliverables include sequence clustering, variant landscape analysis, and competitor watch lists.
Connect With Our Biosequence IP Team
Our experts deliver claim-driven biosequence search and analysis tailored to your development timelines and IP risk profile supporting sequence-based filings, FTO assessments, and IP strength evaluation for biologics and nucleic-acid assets.
Talk To Our Expert
Request a sample redacted biosequence search report to see our approach to sequence listings, identity/similarity analysis, and variant coverage.
