Ensure freedom to operate around a biological sequence

Derwent research guides

Do we have freedom-to-operate around specific biological sequences? Can we commercialize our sequence-based invention in specific markets?

Freedom to operate (FTO) research helps you determine if you can take action around a certain protein or genetic sequence – for example, for testing or commercialization – without infringing on the intellectual property rights of others. The scope of FTO research is narrower than patentability research, but requires greater depth due to the potential impact of mistakes.

GENESEQ on SequenceBase and Derwent Innovation can help minimize the risk of missing an important patent document. Unique sequence coverage in GENESEQ lets you find patents that are not in other databases. Detailed indexing and plain English annotations mean you can quickly understand the relevance of a document. This speeds your analysis and avoids wasting money on unnecessary translations. Complete your due diligence research in Derwent Innovation by analyzing full patent family details and current legal status of patents found with GENESEQ.

Locate patents which contain a biological sequence of interest in GENESEQ

Identify patents related to your biological sequence

The SequenceBase platform includes a choice of sequence homology search options, including BLAST and an optimized Smith-Waterman algorithm.

  1. From the Search screen, select the type of sequence search you want to perform
  2. Enter a sequence into the Search box
  3. Click Search to find patents which contain your sequence or similar sequences

You can change the default settings if required:

  • Algorithm parameters: Change the cut-offs or increase the number of results displayed

Additional Search options: Include text terms or change which sequence databases you search


One of the Additional Search options is exclude documents indexed in GENESEQ from the hits retrieved from additional databases when you search them alongside GENESEQ. Choose this option to remove duplicates and streamline analysis of your results.

Evaluate results to focus on the most relevant documents

Evaluate results to focus on the most relevant documents

Results display sorted by sequence alignment score, with the best matches for your sequence at the top of the list. Use filters to narrow down your results, for example, to see only those where the sequence is claimed.

1.        Click the Documents hyperlink on the top alignment to see a list of patents which contain the sequence which best matches your query sequence
Tip: A 100% match will be the identical sequence to your query

2.        By default, documents display sorted by publication date. Click other columns to sort by other criteria, such as earliest priority


You can link from a document number to the corresponding Record View in Derwent Innovation to read the bibliographic data and abstract or download the full-text PDF file. Open your Account page and select Derwent Innovation as the default for Patent links to. To access all the other “added value” fields such as classes/indexing and patent family, you must sign in to Derwent Innovation.

Use GENESEQ annotations to speed up the review process

To decide whether or not a patent affects your freedom to operate, you need to know for what utility a sequence is being claimed. It can be challenging and time consuming to identify information about a specific sequence, especially given that some patents may contain thousands of sequences and/or be published in different languages. The GENESEQ editorial team writes detailed annotations in plain English to give you the full picture, including:

·         An informative Description encapsulates in one line exactly what the sequence is (species/function)

·         The Comments section provides a brief summary of the invention as a whole and places the sequence in context (novelty/utility)

·         When present, a Features Table pinpoints biologically important regions of the sequence as well as highlighting novel aspects or anomalies



When reviewing a list of documents, click Expand All to display descriptions for all sequences at the same time. GENESEQ records also display the DWPI enhanced title for the patent and keywords and comments specific to the sequence. These specially written annotations help you triage results.


The manual editorial processes used by GENESEQ editors mean that, in contrast with other databases, only GENESEQ captures sequences that are not part of an electronically submitted sequence listing. The GENESEQ editorial team also creates specifically claimed mutant sequences as long as the original, unmutated sequence has been provided. Look out for explanatory editor’s notes at the end of a GENESEQ comments section.

Save relevant documents into folders to generate reports

After evaluating and refining your search results, save any relevant documents into folders. After you save documents, you can generate reports and export them.

  1. Select the checkbox next to the sequence alignments (in Basic display) or documents (in grouped by document display) you want to analyze in Derwent Innovation
  2. Click Add Selected

Export patent numbers for further analysis in Derwent Innovation

You can export data in numerous formats, including Excel, to perform further analyses that you can share with colleagues or clients. The Text export option is specifically for exporting lists of deduplicated patent numbers.

  1. Open the Documents folder
  2. Click in the left hand check box next to the documents you wish to analyze further in Derwent Innovation.
  3. Click Generate Report.
  4. Click the XLSX option
  5. Enter a Report Name and click Generate
  6. Open the Reports tab to download the Excel file which incudes the list of patent numbers

You can upload this list of patent numbers into Derwent Innovation by copying and pasting them.

Locate and review the documents in Derwent Innovation

Upload the list of patent numbers into the publication number search form

1.        From the Dashboard, click on the Patent search button

2.        Click the Publication Number tab

3.        Select the column of publication numbers and copy them (ctrl+C) then paste them into the publication numbers box (Ctrl+V)

4.        Click the down arrow on the box immediately below where it says Specialized Search and select Family Look-Up DWPI

5.        Click Search

Focus on documents that may block your freedom to operate

The filters in Derwent Innovation help you quickly focus on Granted patents, which are the only patents you need to review for freedom to operate research.

1.        Click on the filters menu just above the result set and find the  Grants/Apps one

2.        Check the box beside Grants
Note: You may also want to select Utility models

3.        Click Apply Filters


If you are only interested in specific markets, you may want to focus on specific authorities of interest. Select by the Country Code field, then select the authorities in your target market.


If you do a lot of freedom to operate research in Derwent Innovation, you can set up your result set preferences to include the Grants/apps chart by default. From the Dashboard, click My Account, select the Results Set option under Preferences, select Grants/apps as one of your default Filter Fields, and click Save.=

Focus on patents that are likely still in force

Review the list of granted patent documents. Focus your research on patents that are likely still in force (Alive):

  1. Click on manage columns
  2. Select Dead/Alive and Estimated Expiration Date by checking the boxe beside them and arrange them so they are near the top of the lkist of displaye fields in the column on the right of the screen
  3. Click apply to apoply these settings (they will be remembered going forwards)

Note: Dead/alive and expiration information is provided for guidance only and should not be treated as a definitive legal opinion. Always check a patent’s current status on the patent office website before making investment decisions.

Review details for patents of high interest

The Derwent Innovation record contains an informative DWPI abstract which summarizes the claims in plain English, helping you quickly determine if the patent is a likely threat and whether you need an in-depth study of the claims. Patent claims are available for up to 21 authorities, including English-translated claims for Asian, Latin American, German, French and Russian patents. Patent records include INPADOC legal status for the leading authorities around the world so you can verify our patent status (dead/alive) indicator.

Note that DWPI, Asian, and Latin American content may require additional subscriptions.

1.        To open a record, click the hyperlinked document number on the results set

2.        Click the links in the Jump to line to access portions of the patent record you are interested in (e.g., claims)

3.        Click the right arrow at the bottom of the page to move to the next record

Tip: Press the space bar on your keyboard to quickly mark a record for further review and move to the next record. To access your list of marked records, click Saved Work on the Dashboard, click Work Files, and open the Marked List file displayed at the top of your work files list.