If you’re planning to submit a sequence listing “via epoline,” it’s worth knowing up front that epoline is a legacy brand name. It was the EPO’s original suite of electronic filing tools, launched in the early 2000s. That brand has since been retired: filing today is done through Online Filing 2.0 (OLF 2.0), the EPO’s current web-based filing application, alongside the broader MyEPO Portfolio hub for managing applications and communications. You may still see “epoline” in older documentation, in archived URLs (such as docs.epoline.org, which still hosts current user guides), or in habit among long-time practitioners – but the software you’ll actually use is Online Filing 2.0. This guide uses that current terminology while walking through the process people usually mean when they ask about “epoline.”
Step 1: Know Which Sequence Listing Standard Applies
Before touching the filing software, confirm which WIPO standard governs your listing – this determines the file format entirely:
- WIPO Standard ST.26 applies to any European or international (PCT) application with a filing date on or after 1 July 2022. ST.26 listings are XML files, not plain text.
- WIPO Standard ST.25 still applies to applications filed before 1 July 2022, including any later corrections, rectifications, amendments, or translations of sequence listings tied to those earlier applications.
This split matters because the two standards use entirely different software, file structures and validation tools. Filing an ST.25-format listing for a post-2022 application (or vice versa) will trigger a deficiency.
Step 2: Prepare the Sequence Listing File
For ST.26 applications (filed 1 July 2022 or later)
Use WIPO Sequence, the free desktop tool published by WIPO, to build and validate your listing. It runs on Windows, Mac and Linux. Key points:
- The output must be a single XML file conforming to the WIPO ST.26 DTD schema – no other format is accepted for the sequence listing itself.
- Nucleotide sequences need at least 10 specifically defined nucleotides and amino acid sequences need at least 4 specifically defined amino acids, to require inclusion in the listing.
- Each sequence is numbered sequentially as SEQ ID NO: 1, SEQ ID NO: 2 and so on.
- Mandatory fields include the organism name and a mol_type qualifier for every sequence; the software’s built-in validator will flag missing or malformed entries before you export.
- Always run the final export through WIPO Sequence’s validation function and confirm zero errors before attaching it to your filing. Early versions of the software (2.1.0 and 2.1.1) had a known bug that could silently drop feature tables from exported listings – if you’re using an old cached copy of the tool, update it first.
For ST.25 applications (filed before 1 July 2022, or later corrections to them)
Use BiSSAP, the EPO’s dedicated tool for ST.25-format listings, developed jointly with national offices and the European Bioinformatics Institute. BiSSAP lets you prepare and verify sequences, generate the listing file, import an existing ST.25 listing and run batch verification across multiple listings. If you need to file a correction or amendment to a pre-2022 application’s sequence listing today, BiSSAP – not WIPO Sequence – is the correct tool, even though the filing itself happens in 2026.
Step 3: Handling Divisional Applications
If you’re filing a divisional application whose parent contains a sequence listing, check the date carefully. The EPO’s practice is that a divisional filed on or after 1 July 2022 must include an ST.26-compliant sequence listing, even if the parent application’s original listing was filed in the older ST.25 format. That conversion carries a real risk of inadvertently adding or losing subject matter during the format change.
To manage that risk, applicants can additionally submit the parent’s original ST.25 sequence listing alongside the mandatory ST.26 version, as a safeguard in case discrepancies surface during examination. If your divisional includes converted sequence data, it’s worth having both versions on file and flagging the conversion explicitly in your submission correspondence.
Step 4: Attach the File in Online Filing 2.0
Once your XML (or ST.25) file is ready:
- Open Online Filing 2.0 and start or open the relevant application draft.
- Add the sequence listing as a separate attached file – it is not merged into the main description document. The application form and its supporting documents (request form, description, claims, sequence listing, etc.) are each handled as distinct attachments within the same submission package.
- Follow the EPO’s current file naming convention for sequence listings, which generally incorporates the application number and a version indicator. Because naming conventions can be updated, confirm the exact required format in Online Filing 2.0 itself or the current EPO filing guidance at the time you file, rather than relying on an older naming pattern.
- Use Online Filing 2.0’s built-in validation step before transmission. The software runs a series of checks (structural, formal and file-type validation) and will flag an incorrectly formatted or missing sequence listing before you submit, giving you a chance to fix it rather than receiving a deficiency notice later.
- Review the list of attached documents in the PDF/document viewer pane before sending, to confirm the sequence listing XML appears alongside your other filed documents exactly as intended.
Step 5: Confirm Submission and Deadlines
- If a sequence listing is required but omitted from the initial filing, the EPO generally allows correction within a set period – but treat this as a safety net, not a filing strategy. Missing sequence listings can complicate prosecution, trigger additional fees and in unresolved cases put the application at risk.
- Keep the transmission confirmation and any auto-generated receipt from Online Filing 2.0; these serve as your proof of timely filing, similar to a filing receipt for the rest of the application.
- If the free text portions of the sequence listing (feature descriptions, organism names, etc.) are in a language other than the application’s language of filing, check current EPO language requirements – free text within the listing generally needs to match the language of the application.
If You Hit Technical Problems
The EPO’s Contingency Upload Service exists as a backup filing route for situations where Online Filing 2.0 or the EPO’s systems are temporarily unavailable. It replaced the older fax-filing option. If you’re up against a deadline and the online system is down, this is the fallback path – not email or an informal workaround.
A Note on the “epoline” Terminology
Because “epoline” is no longer the operative brand, anything you read that references epoline-specific screens, smart cards, or the old client-server desktop software may be describing a discontinued workflow. A few markers that content is outdated:
- References to installing standalone desktop software that requires local updates (the older Online Filing client) rather than the current web-based OLF 2.0
- References to epoline smart cards for authentication, since the EPO has been shifting users toward two-factor authentication (2FA) instead of smart-card access
- References to CMS (Case Management System), which was decommissioned in January 2022 in favor of Online Filing 2.0
- References to the Webform Filing tool, which has been phased out as filing volume moved almost entirely to Online Filing 2.0 and MyEPO Portfolio
If your own firm’s internal documentation still calls the process “filing via epoline,” it’s worth updating that terminology internally – it won’t change how the filing works, but it can cause confusion when onboarding new staff or coordinating with the EPO’s current help resources, which are indexed under “Online Filing” and “MyEPO,” not “epoline.”
Quick Pre-Submission Checklist
- Confirmed which standard applies (ST.26 for filings 1 July 2022 onward; ST.25 for earlier applications and their corrections)
- Built the listing in the correct tool – WIPO Sequence for ST.26, BiSSAP for ST.25
- Ran the built-in validator and resolved all errors before export
- For divisionals with a pre-2022 parent, prepared both the mandatory ST.26 version and, as a safeguard, the parent’s original ST.25 listing
- Attached the sequence listing as a separate file in Online Filing 2.0, following the current file-naming convention
- Confirmed the language of any free text in the listing matches the application’s filing language
- Reviewed the full list of attached documents before transmission
- Saved the transmission confirmation/receipt
A Note on Accuracy
EPO filing tools and sequence listing rules have changed substantially over the past few years – the ST.25-to-ST.26 transition, the retirement of CMS and the phase-out of legacy epoline branding all happened within a relatively short window and further tooling changes are likely. Given how procedural this process is and how costly an error in a sequence listing can be, it’s worth confirming current file specifications directly on the EPO’s website or with EPO Customer Services immediately before filing and consulting a European patent attorney for anything beyond a routine, previously-filed sequence type.