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Gene-IT Algorithm Better for IP Searches, Study Says

NEW YORK, Dec. 2-Gene-IT's sequence comparison algorithm works better than public search tools to determine whether a novel gene has already been discovered and patented, finds a report in the December issue of the journal Nature Biotechnology.


Intellectual property searches on DNA or protein sequences can be a tricky matter, write the authors, a group of bioinformatics and legal experts from Pfizer and Gene-IT. Most search algorithms are designed to look for biological similarity, and are tuned for different parameters than the requirements set down by intellectual property law.


BLAST, the public search tool, is homology-based, determining the similarity between genes based on parameters set by the searcher. This flexibility means that two gene similarity searches may deliver different answers. A quirk of patent law further complicates the process: patents are usually granted not just for the sequence itself but for all those closely related to it.


Gene-IT's KERR (also called GenePAST) uses a different strategy to identify similarities. With pairwise alignment, the algorithm identifies sequences that may be similar but of different lengths, as may be the case with splice variants.


This approach is not useful for research, the authors write, since it does not take into account phylogenetic relationships. But because it mirrors intellectual property law, it can be useful for establishing the patent status of a gene.


Gene-IT offers a patent investigation service that uses this algorithm.

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