Searching through databases, manually or using a search engine, is the standard for biological sequence data searches. The advantage of this procedure is the speed with which you can conduct the searches. With a computer and database management software package, it would be possible to scan the database for any relevant matches within minutes. It may take days or even weeks to complete the same task if you want to perform the searches manually.
An issue that is commonly overlooked is missing or inaccurate base pairs. This happens when sequences of bases (such as DNA) are highly repetitive, i.e., within a single genome. For example, humans and chimpanzees share sequences of only seven base pairs. An individual with a similar genetic makeup might well be unable to patent a unique product because of this. In addition, if the sequences are very repetitive, a lot of unrelated products may also be patented. A biological sequence search is important in terms of patent determination.
Why are biological sequence searches important?
Sometimes, biological sequence searches lead to false patent results. For example, some homologous pairs may have been misidentified. Likewise, sometimes sequences are missed due to low quality scans. As these issues are easily resolved, it is easy to see why many researchers prefer to manually search for sequences prior to using the patent database.
Besides being unable to patent genetic diseases, researchers face other concerns with manual searches. One of the main concerns is that they cannot determine whether the sequence described in the patent is unique. For instance, a patent granted to D-shaped genetic diagrams could easily be infringing. Furthermore, sequence searchers do not understand the complicated biological mechanisms involved in natural processes, which makes them relatively limited in their ability to distinguish among potentially patentable biological sequences.
Biomarkers, on the other hand, can automatically identify highly repeated sequences. This greatly improves the accuracy of these searches. It also helps in determining whether the sequences described in the patent specification are truly unique. In contrast to biological sequence searches, an FTO search allows for highly repetitive DNA sequences to be identified.
An FTO search requires input that is highly specific, and it produces highly specific results. The majority of FTO searches are performed on publicly available data. This is in part because it is difficult to determine the exact molecular mechanisms involved in highly repeating sequences. Another limitation of FTO search is that it can only be performed on highly replicated sequences. If the sequence is highly replicated, then it can be excluded from a patent based on unproven mechanisms.
A BTO search queries a database that contains highly specific and orthologs databases. Because the retrieved sequences are highly specific, it is possible for a searcher to retrieve only those features of a biological system that are needed for their patent searches. Another limitation of a BTO search is that it does not search for highly repeated sequences. Therefore, if a specific, previously unknown sequence is not present in the database, a searcher may not be able to obtain useful information.
Biochemical and biological sequence searchers typically use the databases provided by the Protein Data Bank (PDB) and the Gene Ontology Database (GOD). These databases have been established through years of collaboration between biotechnological and pharmaceutical researchers. In addition, many of these databases were established specifically to serve this particular purpose. For example, the PDB was developed in order to improve the accuracy of drug development efforts. The GOD works to interpret the results of genetic studies in order to provide patentable claims. The databases allow searchers to employ a wide range of biological and chemical terms to search for and identify biological structures or processes.
While BTO and FTO searches are useful for producing comprehensive results, they miss certain information that may be critical in determining the invention’s scope. Biochemical and biological sequence searchers should ensure that the databases they access contain both orthology and synonym databases. This is because it is sometimes necessary to distinguish between two unrelated biological structures when the goal is to determine whether the invention is eligible for patentability. Further, it is often necessary to determine if the claimed invention is indeed unique or not, particularly where related inventions are involved.
This is one of the key reasons why developers of patents typically include a database of prior art that is reviewed and used in the overall search process. It is also important to ensure that the research used in generating the patent does not alter or dilute the scope of protection. This can be done by ensuring that the databases used in the overall search process comprise only highly informative databases. In addition, it is also important that sequences are classified properly. For example, biological processes such as the extraction of nucleic acids from biological samples and construction of gene-expression systems are generally classified as processes rather than mere procedures. Finally, it is important that the classification of the sequence does not provide scope for what would be considered illegal conduct since the claims may be based on valid biological processes that would otherwise fall outside the claims’ protection.