PatSeq Explorer

The PatSeq Explorer offers a dynamic, embeddable, and multi-level view of mapped patent sequences on a genome of a specific organism. We currently offer patent sequences mapped onto the human, mouse, maize, rice, and soybean genomes, with other genomes to be mapped soon.

PSEgenomesYou c

 

an view the PatSeq Explorer here: https://lens.org/lens/bio/patseqexplorer

Sequence Download

You can now download mapped sequences from the various view levels freely.   For terms of use see this link.

For mapped data, please cite

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

The sequence download option is found at the bottom of the page and will download those sections based on your imposed filters or search options up to 10,000 sequences per download. The downloaded data will be in FASTA format. “Applications: Peptides (all) “means all amino acid sequences that are disclosed (regardless of whether they are referenced or not in the claims) in published patent applications; “Applications: Peptides (in Claims) means a subset of the earlier collection and only those sequences that were referenced in the claims of published patent documents.  If you still have any questions, please email us at support@cambia.org.

 

Filtering & Searching Options

On the left side panel of the PatSeq Explorer , a large number of collapsable filtering and searching options are available for your use.  You may want to explore the wide range of similarity (100-90%) and coverage (100-50%) thresholds  to view patenting trends at either the genome or chromosome levels.  Remember that you are looking at mapped sequences that are either referenced  in patent documents (grants or published applications) or simply disclosed in these documents regardless of whether they are referenced or not in the claims.  You can choose to view nucleotide or peptide sequences.  You may choose to view the genome map based on sequence counts or patent documents counts (these counts are redundant since one patent document may contain one or millions of sequences), select the publication/filing years of interest (or watch an animation of the sequences published/filed over time), filter by jurisdictions, filter by sequence length, or filter by the declared species.

You can also filter the results using search tools that are based on the patent attributes.  For example, you can search for keywords that appear in the title, abstract or Claims section of the patent, you can search by applicant, owner, or inventor, or even publication number or classification.   While using the human genome map, you can as well search by disease name (based on the OMIM database) at the chromosome level.

Genome view

The default view of the PatSeq Explorer shows each of the 22 autosomal chromosomes and each of the 2 sex chromosomes in the human genome. The bar chart attached to each of these chromosomes depicts the number of mapped patent sequences per 10 Mb interval chromosomal  thresholds. Hovering over each bar will give you statistical information about the number of mapped sequences and their corresponding patent documents at that specific location.  You can filter and view whole genome patenting trends at various similarity or Coverage thresholds.  Similar mapping metrics were used in the other genomes.

Chromosome View 

By clicking on any of the tooltips associated with a chromosome, you can zoom in and view each chromosome separately.  In this view, mapping of patent sequences is more granular and spaced at 2MB bins along each chromosome.  By clicking on each bar, you would be able to obtain a rough idea of how many sequences are disclosed per that region, download them, and/or link to their corresponding patent documents in the Lens.

If you are interested in looking at diseases and traits associated with that chromosome in the human genome, hover over the chromosome itself and you can view the details of the OMIM database with links directly to that public database.   If you are keen on a particular chromosomal region, you can zoom in  further to view results in our PatSeq Analyzer, a newly modified genome viewer that would enable you to navigate and analyze patent sequences at the gene region or detailed sequence levels.