Modification

Granular control of modification-based sequence searching is often a process with a huge time cost. The Chemical Modification search is here to address that issue. This video will guide you through how to use the Chemical Modification Tool to run advanced patent sequence searches based on chemical modifications rather than sequence alone. It covers building precise modification queries using Boolean and positional logic, adding custom or ontology-based modifications, refining search scope, and analyzing modification-rich patent results to support faster FTO, competitor intelligence, and therapeutic innovation research.

• The tool is designed for cases where the therapeutic value comes from sequence modifications, not just a novel sequence.
  
  It helps replace slow, manual patent searching with a more structured way to find modification data.
  
  This is introduced as a first-of-its-kind Chemical Modification tool.
• Add a title for your search.
  
  Define the sequence length.
  
  Use a smaller length for things like siRNAs.
  
  Use a larger length for broader oligonucleotide searches.
  
  This sets the foundation for the modification query.
• Choose how modifications should be combined using Boolean connectors:
  
  OR
  
  AND
  
  NOT
  
  These connectors let you include or exclude specific modifications of interest.
  
  This step helps narrow the search to the most relevant chemical patterns.
• You can define a modification in three ways:
  
  Type it directly into the search box (for example, glycosylation).
  
  Browse the ontology to select a broader or more specific modification category.
  
  Use Draw Structure to open the chemical drawing tool and enter a custom structure.
  
  This gives flexibility depending on how precise your search needs to be.
• After entering modifications and positions, refine the logic using the position rules.
  
  Any vs. All:
  
  Any = at least one of the listed positions must have the modification.
  
  All = every listed position must have the modification.
  
  Contain vs. Match:
  
  Contain = the modification must be present at the specified positions.
  
  Match = only that modification can be present at those positions.
  
  All Match gives the most precise control over the query.
• You can optionally upload a query sequence, similar to a traditional sequence search.
  
  If you do not add a sequence, the positions you defined will apply to the subject sequences returned in the results.
  
  This lets you search by modification pattern even without a starting nucleotide or protein sequence.
• Since no sequence was entered, manually choose whether to search:
  
  the nucleotide database, or
  
  the protein database.
  
  Then choose the document scope:
  
  Claims only, or
  
  broader patent/non-patent coverage, including title, abstract, claims, and description.
  
  In the example, all scopes are left enabled before running the search.
• The results page looks similar to a traditional bio-sequence search, but with key modification-focused differences.
  
  At the top, the overview shows how often the searched modifications appear across the hit sequences.
  
  In the example, the modification appears in 100% of the hit sequence list.
• Hover over a sequence to highlight the specific modification mentioned.
  
  Click on a hit to view the modification details in that patent document.
  
  You can see:
  
  the modification you searched for, and
  
  other modifications present in the same document.
  
  This helps you understand the full modification context of each hit.
• Open the Modification Browser to isolate and review all modifications across the returned patent documents.
  
  This lets you see:
  
  the initial query sequences,
  
  all modification types found, and
  
  the broader modification landscape.
  
  Use the dropdown to refine the list and analyse the sequence space more deeply.
• The tool is especially useful for:
  
  FTO (freedom to operate),
  
  competitor intelligence, and
  
  innovation tracking.
  
  It provides:
  
  faster searches,
  
  deeper insight into modification patterns, and
  
  more confident therapeutic strategy decisions.