This track shows genome matches to biomedical sequences submitted with patent application
documents to patent offices around the world. The sequences, their mappings, and selected
patent information were graciously provided by PatSeq, a search tool part of The Lens,
This track contains more data than the NCBI Genbank Division "Patents", as the
sequences were extracted from patents directly.
Display Convention and Configuration
The data is split into two subtracks: one for sequences that are only part of patents that
have submitted more than 100 sequences ("bulk patents")
and a second track for all other sequences ("non-bulk patents").
A sequence can be
part of many patent documents, with some being found in several thousand patents.
This track shows only a single alignment for every sequence, colored based on
its occurrence in the different patent documents and using a color schema similar to The Lens.
Based on the first sequence match, the four different item colors follow this priority ranking in
|the sequence is referenced in the claims of a granted patent|
|the sequence is disclosed in a granted patent|
|the sequence is referenced in the claims of a patent application|
|the sequence is disclosed in a patent application|
Sequences referenced in the claims section of a
patent document define the scope of the invention and are important during
litigation. Therefore, they are given priority in the color scheme. Patent
grant documents form the basis of patent protection and are prioritized over
Hover over a feature with the mouse to see
the total number of documents where the sequence has been referenced, how many
of these documents are granted patents and how often the sequence has been
referenced in the claims. A randomly selected document title is also shown in
Clicking on a feature will bring up the details page, which contains information about
the sequence and alignment of that feature.
The link at the top of the page opens the PatSeq Analyzer with
the chromosomal region covered by the feature that was clicked. The PatSeq Analyzer
is a specialized genome browser that allows for the viewing and filtering of patent
sequence matches in detail.
The next section of the details page is a list of up to ten patent documents that include this
sequence, with the number of occurrences within each document in parentheses.
This is followed by up to thirty links to patent documents. The patent documents listed in these
sections are displayed in order of the number of sequence occurrences in the document. Shown below
these are the links to the sequence in The Lens, in the format
"patentDocumentIdentifier-SEQIDNO (docSequenceCount)". The "SEQ ID NO"
is an integer number, the unique identifier of a patent sequence in a patent
document. When a protein sequence has been annotated on a nucleotide sequence,
the "SEQ ID NO" contains the reading frame separated by a ".", e.g.
"1.1" would indicate the first frame of SEQIDNO 1.
The total number of sequences submitted with the patent document ("docSequenceCount") is
shown in parentheses after the SEQIDNO. The links to the sequence are separated into the
categories "granted and in claims", "granted", "in claims"
and "applications" (=all others). Sequence identifiers link to the respective pages on PatSeq. A maximum of thirty documents
are linked from this page per category listed in order of the number of sequence occurrences;
please use PatSeq Analyzer to view all matching documents.
The score of the features in this track is the number of documents where the
sequence appears in the claims. For example, by setting the score filter to 1, only
sequences are shown that have been referenced at least once in the claims.
More than 96 million patent document files were collected by The Lens. The
sequences were extracted and mapped to genomes with the aligners BLAT and BWA. The minimal
identity of the query over the alignment is 95%. Note that for hg19, no patents are shown
on chrM, as the mitochondrial chromosome used for the mapping was the one from
the Ensembl genome FASTA files.
Thanks to the team behind The Lens,
and Deniz Koellhofer, for making these data available.
Send suggestions on the way data in this track is visualized to our support
Questions on the data itself are best directed to
The raw data can be explored interactively with the Table Browser.
For automated download and analysis, the genome annotation is stored in a bigBed file that
can be downloaded from
our download server.
The files for this track are called patNonBulk.bb and patBulk.bb. Individual
regions or the whole genome annotation can be obtained using our tool bigBedToBed
which can be compiled from the source code or downloaded as a precompiled
binary for your system. Instructions for downloading source code and binaries can be found
The command to obtain the data as a tab-separated table looks like this:
bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/hg19/bbi/patNonBulk.bb -chrom=chr5 -start=1000000 -end=2000000 output.tsv
A full log of the commands that were used to build this annotation is available
from our database
build description. In this text file, search for "patNonBulk" to find the right section.
Editorial: The patent bargain
Nature. 2013 Dec 12;504(7479):187-188.
Nat Biotechnol. 2006 May;24(5):474.
Jefferson OA, Köllhofer D, Ehrich TH, Jefferson RA.
Transparency tools in gene patenting for informing policy and practice.
Nat Biotechnol. 2013 Dec;31(12):1086-93.