Introduction
Patent applications disclosing nucleotide or amino acid sequences must be accompanied by a standardized “sequence listing” – a structured file cataloging every disclosed sequence, typically referenced in the claims as “SEQ ID NO: X.” For searchers, examiners, competitors and licensing teams, these listings are a goldmine: they let you determine whether a specific gene, protein, or fragment has already been claimed, published, or disclosed as prior art – something a keyword search alone often cannot reveal reliably, since sequences are rarely described adequately in prose.
Espacenet (the European Patent Office’s public search platform) and PATENTSCOPE (WIPO’s public search platform) are the two most widely used free tools for accessing and analyzing these listings. This article explains the underlying standard, how to locate sequence data on each platform and how to actually work with it once retrieved.
1. The Underlying Standard: WIPO ST.26
Before working with sequence listings, it’s important to understand which format you’re dealing with, since this determines what file type you’ll retrieve and how you can search it.
- A new global sequence listing standard, WIPO Standard ST.26, came into force on 1 July 2022, with all WIPO member states implementing it simultaneously at the international, regional and national levels. Under ST.26, sequence listings must be presented as a single file in XML format, rather than the plain-text TXT format used under the older ST.25 standard, with the XML format intended to facilitate searching of the sequence data, particularly in public databases.
- The application’s filing date determines whether a sequence listing must comply with ST.25 or ST.26: applications filed on or before June 30, 2022 remain under ST.25, while applications filed on or after July 1, 2022 must use ST.26 – and this is governed strictly by filing date, not priority date.
- A sequence qualifies for inclusion when a nucleotide sequence contains more than 10 specifically defined residues, or an amino acid sequence contains more than 4 specifically defined residues.
- One consequence of the shift to XML is that the sequence listing is no longer submitted in a human-readable txt format, which has made direct visual review harder without the right viewing tools – a point directly relevant to how you’ll need to view the file once you’ve located it on either platform.
Because of this transition, when analyzing an older application (pre-July 2022) you’ll typically be working with a flat ST.25 .txt-style listing, while a post-2022 application will hand you an ST.26 XML file that needs a viewer to read comfortably.
2. Accessing Sequence Listings via Espacenet / EPO Tools
Espacenet itself (the general public search interface) is primarily a bibliographic and full-text search tool; the EPO’s dedicated mechanisms for retrieving the actual sequence listing files sit in two related places: the European Publication Server and EP full-text search.
a. Via the European Publication Server (document ZIP file)
Since sequence listings according to ST.26 no longer feature in the PDF of the A-publication, they are instead included in the ZIP file of the corresponding document on the European Publication Server. To retrieve one:
- Locate the publication on the European Publication Server (or via the European Patent Register’s “All documents” tab).
- Download the ZIP file associated with the publication.
- Extract it – the sequence listing will appear as a standalone XML file compliant with ST.26, separate from the main PDF document.
b. Via EP Full-Text Search
Sequence listings can also be accessed using EP full-text search: open the platform, select EP full-text search from the list of available tools and in the query field enter a search such as PSL = YES – where PSL stands for “Presence of Sequence Listing.” After running the search and navigating to the results page, click “More” in the document window to see additional available data, then select the sequence listing to display or download it.
This PSL = YES field is particularly useful when you want to build a result set limited only to applications that actually carry a sequence listing – filtering out the large majority of biotech-adjacent filings that reference sequences in prose but don’t formally disclose a compliant listing.
c. Practical notes on the EPO side
- Because Espacenet’s general search doesn’t index the raw sequence data itself (i.e., you cannot type in a nucleotide string and search Espacenet the way you would a bibliographic term), sequence-level similarity searching is not performed on Espacenet directly – it’s a retrieval/access tool, not a sequence-alignment engine.
- The EPO recommends that applicants use WIPO Sequence, downloadable free of charge from the WIPO website, to prepare ST.26-compliant sequence listings – and that same free tool is the most practical way for a searcher to open and browse a downloaded ST.26 XML file in human-readable form (see Section 4 below).
3. Accessing Sequence Listings via PATENTSCOPE
PATENTSCOPE has built out considerably more sequence-specific functionality than Espacenet, reflecting WIPO’s role as steward of the ST.26 standard itself.
a. Platform background
PATENTSCOPE is a free, public patent search system covering more than 120 million patents across more than 80 national collections plus PCT applications. Its chemical and sequence-related functionality has been added incrementally: basic chemical search was introduced in 2016, substructure chemical search in 2019, Markush chemical search in 2020 and – most relevantly here – ST.26 Sequence Listing functionality in 2021.
b. Locating and viewing sequence listings
- WIPO has introduced the ability to visualize ST.26 sequence listings directly in an internet browser from PATENTSCOPE, so that users no longer have to download the XML sequence listing and import it into WIPO Sequence separately. This is a meaningful convenience advantage over Espacenet’s ZIP-download-only approach – you can inspect sequence annotations (organism, molecule type, feature locations) inline without leaving the browser.
- On an individual application’s detail page in PATENTSCOPE, sequence data appears as a dedicated tab/section when a compliant listing is present, alongside the standard bibliographic, description and claims tabs.
c. Sequence search / similarity search functionality
Because a sequence listing on its own is only useful if you can search within it (rather than just read it), the more valuable capability is sequence similarity search:
- WIPO documentation describes PATENTSCOPE and INSDC (International Nucleotide Sequence Database Collaboration) databases together with sequence similarity search tools as a core part of the sequence listing ecosystem, meaning PATENTSCOPE is positioned to interoperate with public genomic databases (GenBank, EMBL, DDBJ) rather than functioning in isolation.
- Because ST.26 reuses public genomic database vocabularies and structures and was designed to facilitate integration with public sequence databases, sequences disclosed in recent patent filings are increasingly cross-searchable against GenBank-style records – useful for confirming whether a claimed sequence corresponds to a previously known natural or public sequence.
4. Working With the Retrieved Files: WIPO Sequence and Viewers
Once you’ve pulled an ST.26 XML sequence listing from either platform, you generally have three options for actually analyzing it:
- View inline in PATENTSCOPE (post-2021 filings) – fastest for a quick check of what sequences are disclosed and their basic annotations, without any software installation.
- Open with WIPO Sequence (the free desktop application from WIPO) – WIPO Sequence is a global software tool that enables patent applicants to prepare amino acid and nucleotide sequence listings compliant with WIPO Standard ST.26 and includes the ability to upload, view and print XML sequence listings in a human-readable format even if you weren’t the one who authored them. This is the most reliable way to browse an ST.26 XML file downloaded from the EPO’s ZIP archive, since Espacenet has no built-in XML viewer of its own.
- Third-party sequence search services – for serious freedom-to-operate or patentability work, commercial sequence-search providers run alignment algorithms (BLAST, percent-identity, fragment search) across combined patent and non-patent sequence databases, covering USPTO, INPADOC/EPO and WIPO/PCT filings from roughly 1980 to the present, together with open-access databases like GenBank, EMBL and DDBJ. These are useful when Espacenet/PATENTSCOPE access alone won’t answer a true similarity question (“does any patent disclose a sequence ≥90% identical to mine?”).
5. Practical Workflow for a Sequence Listing Search
A typical due-diligence or prior-art workflow combining both platforms might look like this:
- Scope the search – identify whether you’re searching for an exact sequence match, a close variant, or simply confirming presence/absence of any sequence listing on a given family of applications.
- Filter for presence of a listing – on EP full-text search, run PSL = YES combined with your other bibliographic/classification criteria to isolate applications that actually carry compliant sequence data.
- Retrieve the file:
- Post-July-2022 EP filings → ZIP file from the European Publication Server, or inline viewing on PATENTSCOPE if the family includes a PCT/WO publication.
- Pre-July-2022 filings → expect an ST.25 plain-text listing, typically still attached to the application file wrapper.
- Cross-check on PATENTSCOPE – search the same family or a related sequence string via PATENTSCOPE’s sequence tools to check for broader international coverage and to leverage its visualization and cross-database linkage to INSDC records.
- Open in WIPO Sequence for detailed annotation review – molecule type, organism, feature locations and any linked sequence identifiers (SEQ ID NO mapping back to claim language).
- Run a similarity search if the goal is more than presence/absence – i.e., confirming novelty or freedom-to-operate against a specific sequence – using a dedicated sequence-search service, since neither Espacenet nor PATENTSCOPE currently performs true BLAST-style alignment search natively across the full corpus for a public user.
- Document findings against claim language – always map any sequence match back to how it’s actually recited in the claims (exact sequence, percent identity threshold, functional fragment, etc.), since the sequence listing itself is descriptive support, not the claim scope.
6. Common Pitfalls
- Assuming Espacenet indexes raw sequence strings – it does not; it’s a retrieval mechanism (ZIP/PSL flag), not a sequence-alignment search engine.
- Confusing ST.25 and ST.26 file formats – an older TXT-format listing won’t open correctly as XML in WIPO Sequence’s newer viewer without conversion and vice versa.
- Treating “presence of a sequence listing” as equivalent to “sequence is claimed” – many listings include sequences referenced only in the description (e.g., primers, controls) that are not recited in the claims at all.
- Overlooking family-wide differences – a PCT/WO publication and its national phase EP equivalent may have identical sequence content but be indexed differently across PATENTSCOPE and Espacenet; checking both is often necessary for complete coverage.
- Relying solely on free-tool visualization for high-stakes FTO work – inline viewers are excellent for quick checks but are not a substitute for a proper similarity/alignment search when the question is whether a specific sequence has been disclosed elsewhere, even in modified form.
Conclusion
Espacenet and PATENTSCOPE approach sequence listing access from different angles – Espacenet (through EP full-text search and the European Publication Server) is built around document retrieval, using the PSL = YES flag and ZIP-file extraction to surface ST.26 XML listings, while PATENTSCOPE has built more sequence-native functionality directly into its interface, including inline XML visualization and closer integration with public sequence databases. Neither platform alone provides true sequence-alignment search at scale, so for prior-art or freedom-to-operate work involving actual sequence similarity (rather than mere presence of a listing), pairing these free tools with WIPO Sequence for file review and a dedicated similarity-search service for alignment work remains the most reliable combination.