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Bio sequence patent search is a unique type of life-science search requiring specialist tools and industry knowledge. In our previous webinar, Questel’s Juliane Wissuwa discussed effective patent search techniques for biological sequences and the benefits of choosing a specialist search tool. Here, we summarize the key points from her presentation.
Biological sequences (or bio sequences) are single, continuous molecules of nucleic acid or amino acid, forming DNA/RNA or proteins and carrying instructions for the development, functioning, growth, and reproduction of organisms.
Bio sequences contain information for enzymes, antibodies, hormones, inhibitor molecules, or positioning molecules for genetic modification (CRISPR/Cas). They are captured as patents across various industries and academic sectors, including the pharmaceutical industry, biotech, agrochemical, food, and enzymes sectors, as well as by technology transfer offices (TTOs) and research and development (R&D) institutes.
Example bio sequence string for a DNA sequence (top) and translated into a protein (bottom).
These patents not only cover drug-related inventions such as biologics, vaccines, and drugs, but also innovation in diagnostics and biocatalysts (biotech), fermentation, modified crops, plant and animal breeding (agriculture), and flavoring or enhancer molecules (food).
However, there is no “standard” bio sequence patent, as the strings vary in length, from a few residues to several million, and patents may capture only a small fragment or a whole genome.
The Unique Challenges of Bio Sequence Patent Searching
While captured as a consecutive series of letters (as illustrated above), bio sequences are rarely displayed as such in patent claims. Most often, they are numbered or displayed in tables (as shown below, top) or referenced in the attachments as a table or Annex.
In addition, a patent may reference an entire bio sequence or a subsequence, as can be seen in the example below, where it references specific amino acid residues:
Finally, a patent may claim the bio sequence or simply disclose it for information.
Bio Sequence Patent Search Specifics
“Normal” patent searches are semantic searches, using keywords and synonyms combined with Boolean operators and truncations and/or wildcards to narrow the search scope. However, this type of search is not applicable for bio sequence patent searching, as it raises two issues:
Firstly, as explained above, bio sequences are often not directly displayed as such in the patent text but rather added as supplements/annexes or within tables;
Secondly, bio sequences can contain small variations within the letters but still have the same functions, making it difficult—not to mention time-consuming—to anticipate all variations with truncations/wildcat searches.
Instead, you need a dedicated tool that enables you to search according to the specific bio sequence format (FASTA) and adapt search parameters according to unique bio sequence parameters, such as length.
How to Perform a Bio Sequence Patent Search on Orbit Intelligence
Orbit BioSequence is a dedicated tool for comparing similarity between sequences. As shown below, it enables users to search biological sequences in the FASTA format, either as nucleic or amino acid; use the same sequence type in multiple searches; and adapt search parameters according to the specific bio sequence, including:
Query length: long/short/motive;
Appropriate database: nucleotide or protein database or both for the most exhaustive results;
Subject sequence length: limit length to look for a short sequence as a primer (as you may not need to search for whole genome information).
If you only receive a limited number of results, you may be able to review them manually. However, many bio sequence patent searches will bring up hundreds or even thousands of results, hence Orbit BioSequence includes specialist filters to help eliminate the noise and narrow or concentrate the results.
The Biosequence Filter enables you to filter according to the percentage match of the query or subject, the number of errors or gaps, and the subject or alignment lengths, as well as to limit your search to the claims, so that patents are only displayed that claim (rather than reference) the sequence.
The Patent Filter helps to inform freedom-to-operate searches byenabling you to filter by legal status, application year, and publication countries. This ensures you don't necessarily need to search worldwide to identify an identical or similar sequence.
The Relevancy Filter enables you to search by keyword (semantic), international patent classification (IPC) number, and assignee or even extract patents involved in litigations, oppositions, licensing, etc.
The Advanced Search option enables you to combine bio sequence searches with keyword searches to reduce noise without losing valuable bio sequence information.
Free and Paid Databases—What's the Difference?
There are free and licensed databases available for bio sequence patent search, but there are several differences to keep in mind.
Search Free databases tend to focus on specific websites as sources for bio sequence patents, meaning coverage is often limited and may not be up-to-date. Paid databases feature a broader and more accurate coverage of patent sequence data as they harvest information directly from patent offices.
Integration Free databases have limited options for filtering results by patent information, with barely any data about patents in many instances. Paid databases include advanced filtering options developed specifically for patent professionals, including the ability to combine keyword and full-text searches.
Display Free databases are typically not user-friendly and have limited available sequence-matching information. Paid databases provide a more straightforward and comprehensive display of sequence alignments making them easier to screen.
Data export Free databases do not facilitate data exports or provide limited formatting options. Paid databases offer different formats for data exports, including the ability to customize reports.
Support Free databases may not require a fee, but they also do not provide any support. Paid databases provide that extra layer or support a part of the license fee, so you can ask the supplier questions, get guidance to improve your search, and even ask them to perform a search for you if you’re uncertain or short on resources.
Bio Sequence Patent Search Best Practices
To produce comprehensive, accurate, and precise bio sequence patent search results, you need to understand both the specifics of patent drafting and patent searching.
Using a dedicated bio sequence patent search tool, such as Orbit BioSequence, will provide you with the data, search parameters, and filters you need to obtain and refine results.
As important when searching bio sequence data, you need to consider the entire patent to obtain complete search results.
Finally, outsourcing prior art searches to a BioSequence Subject Matter Expert can provide you extra support. Before you issue a legal opinion or file an application or defense against infringement, let us find the quality search results you need.
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