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Background  The number of patents associated with genes and proteins and the amount of information contained in each patent often present a real obstacle to the rapid evaluation of the novelty of findings associated to genes from an intellectual property (IP) perspective. This assessment, normally carried out by expert patent professionals, can therefore become cumbersome and time consuming. Here we present PatentMatrix, a novel software tool for the automated analysis of patent sequence text entries.    Methods and Results  PatentMatrix is written in the Awk language and requires installation of the Derwent GENESEQ™ patent sequence database under the sequence retrieval system SRS.  The software works by taking as input two files: i) a list of genes or proteins with the associated GENESEQ™ patent sequence accession numbers ii) a list of keywords describing the research context of interest (e.g. 'lung', 'cancer', 'therapeutics', 'diagnostics'). The GENESEQ™ database is interrogated through the SRS system and each patent entry of interest is screened for the occurrence of user-defined keywords. Moreover, the software extracts the basic information useful for a preliminary assessment of the IP coverage of each patent from the GENESEQ™ database. As output, two tab-delimited files are generated which provide the user with a detailed and an aggregated view of the results.  An example is given where the IP position of five genes is evaluated in the context of 'development of antibodies for cancer treatment'    Conclusion  PatentMatrix allows a rapid survey of patents associated with genes or proteins in a particular area of interest as defined by keywords. It can be efficiently used to evaluate the IP-related novelty of scientific findings and to rank genes or proteins according to their IP position.

PatentMatrix: an automated tool to survey patents related to large sets of genes or proteins