The PatSeq Analyzer is a modified genome viewer tool that is now a stand alone facility but links to PatSeq Explorer to give you a full view on a patent sequence details. It is based on the open source HTML5/SVG genome maps browser by the Computational Medicine Institute, Prince Felipe Research Centre, Valencia, Spain.
How To Use
The Analyzer allows you to zoom in to the details of particular patent sequence entries mapped onto a gene region, refine mapping position, and compare all patenting trends within that particular mapping position either at a gene region or at the detailed sequence level. The Analyzer also enables free sequence downloads.
In addition to the dedicated patent sequence tracks available in PatSeq Analyzer that are based on sequence type and sequence location within patent documents, the app provides feature tracks from public genome annotation datasets (including SNPs and gene/transcripts).
The tool also provides a gene and SEQ ID search capability wherein you can locate a gene of your interest on a specific chromosome and analyze or even predict patenting activities around it or search a SEQ ID range based on patent and SEQ ID numbers. For example see below patenting activities surrounding BRCA1 gene on Chromosome 17 of the human genome using mapped sequences that are either referenced in the claims of granted patents or simply disclosed in granted patents.
To view integrated patent and sequence information, just hover over a mapped patent sequence (SEQ ID No patent document details) in the appropriate PatSeq track and view a summary view re that sequence in a tooltip. Clicking on the tooltip, you can then view the sequence information within the context of its corresponding patent document attributes including the claims. The tool enables you to compare several patent sequences and analyze the claims from various patents simultaneously. For example of tooltip and popup integrated view, please see below:
All tracks are modular and can be turned on and off. Conversely, all views in PatSeq Analyzer are embeddable.
Filtering & Searching Options
On the left of the PatSeq Analyzer are a large number of collapsable filtering and searching options. These include filtering results by % Similarity, Coverage, Sequence Length, Declared Species or by document years and/or jurisdictions. You can search for specific publication numbers, sequence ID numbers, gene names, or SNP names.
Sequence Download
You can now download freely selected sequences from a section of any of the mapped genomes you are looking at in the PatSeq Analyzer . For more details on the terms of use, please see this link. Sequence download option can be found right above the genome browser and will only download those sections filtered above. To download larger sections (i.e. an entire chromosome or the entire genome) use the sequence download tool on the PatSeq Explorer. Please cite any of the following three publications based on their relevance to the data downloaded;
Jefferson, O.A., Köllhofer, D., Ehrich, T.H. & Jefferson, R. A. Transparency Tools in Gene Patenting for informing policy and practice, Nature Biotechnology 31,1086–1093 (2013) http://www.nature.com/nbt/journal/v31/n12/full/nbt.2755.html
Or
Jefferson, O.A., Köllhofer, D., Ehrich, T.H. & Jefferson, R. A. Gene patent practice across plant and human genomes, Nature Biotechnology 33 (10) 1033-1038 (2015) http://www.nature.com/nbt/journal/v33/n10/full/nbt.3364.html
Or
Jefferson, O.A., Köllhofer, D., Ehrich, T.H. & Jefferson, R. A. The ownership question of plant gene and genome Intellectual properties, Nature Biotechnology 33 (11) 1138-1143 (2015) http://www.nature.com/nbt/journal/v33/n11/pdf/nbt.3393.pdf
FAQ
When I click on PatSeq Analyzer after doing a sequence search, would PatSeq Analyzer track and find my sequence?
PatSeq Analyzer does not track your sequence, when you enter the app, you can search either by gene name or by the publication number along with the sequence id. For an example, we will use the sequence discussed in this blog https://cdsouthan.blogspot.com/2018/12/looking-through-lens.html to find the three sequences disclosed in US 6060277 A patent document, all we need to do is search by publication number US 6060277 A and SEQ ID 1-3.
And by clicking on the sequence found (marked in red), we will be able to see it aligned in that chromosome 1 region 40.6-40.8 Mbs.