Patents and Applications Over Rice Sequences

Whole Genome View of Nucleotide Sequences from U.S. Patents that are Highly Similar to Rice Genome Sequences

To generate the data for this application, sequences were extracted from both US applications and US granted patents. The extracted sequences were then compared to the genome using MEGABLAST, and are shown here using the Gbrowse genome browser.

Granted U.S. patents are designated by the blue arrow heads, and applications are designated by the grey shading on each of the 12 chromosomes. The darker the shading, the more patent application sequences there are with homology to that particular section of the chromosome*.

The figure below is interactive! Click on a chromosome to see more detail about rice patents and patent applications, and then shift + click to see the region in greater detail.

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U.S. Applications that Recite Nucleotide Sequences in Claims

The blue bars in the plot below represent the total number of newly-filed U.S. patent applications per month that recite nucleotide sequences in their claims. The nucleotide sequences can be from any organism.  The applications were plotted by their filing date. In order to be included in the graph, the sequence had to be at least 150 base pairs in length and have a BLAST E value that was less than 1e-200. Note that there is an 18 month delay between when an application is filed and when it is published, so the data for the last 18 months is incomplete.

Summary

This plot indicates that the number of applications that recite nucleotide sequences in the claims appears to be have decreased after peaking in 2002.

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U.S. Applications that Recite Oryza sativa Nucleotide Sequences in Claims

The blue bars in the plot below represent the number of US patent applications filed per month that recite at least one Oryza sativa nucleotide sequence in their claims. The applications are plotted by their filing date. In order to be included in the graph, the sequence had to be at least 150 base pairs in length and have a BLAST E value that was less than 1e-200. Note that there is an 18 month delay between when an application is filed and when it is published, so the data for the last 18 months is incomplete.

Summary

Similar to the previous page showing all U.S. applications, this plot indicates that the number of applications that recite Oryza sativa nucleotide sequences in the claims appears to be decreasing. The number of applications reciting rice sequences appears to have peaked in 2003.

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Granted U.S. Patents: Number of Sequences Oryza sativa Sequences Referenced in Claims per Genome Segment

The blue bars in the plots below represent the number of sequences recited in the claims of U.S. patents that match a given 300 kilobase pair (kbp) segment of the rice genome. By match, we mean that the patent sequence is at least 150 base pairs in length and aligns with a rice genome sequence with a BLAST E value of 1e-200 or less. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that the majority of the 300 kbp segments do not match any sequences that are recited in the claims of granted U.S. patents. For the segments that have one or more matches, there are no more than eight matched sequences per segment. Chromosome 3 has the most sequences matches with 55, and chromosome 9 had the fewest with 13.

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Granted U.S. Patents: Number of Patents that Claim Oryza sativa Sequences per Genome Segment

The blue bars in the plots below represent the number of granted U.S. patents that recite sequences in claims that match each 300 Kbp segment of the rice genome. By match, we mean that the patent sequence is at least 150 base pairs in length and aligns with a rice genome sequence with a BLAST E value of 1e-200 or less. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that the majority of the 300 kbp segments do not have any patents with recited sequences that match the rice genome. For the segments that have one or more patents, the highest number of patents is six. Chromosome 3 has the most patents with 39.

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Granted U.S. Patents: Percent Coverage by Oryza sativa Patent Claims per Genome Segment

The blue bars in the plots below represent the percent of coverage of a given 300 kbp segment by granted U.S. patents. For example, if an entire 300 kbp segment matched sequences that were recited in claims US patents, the plot would read 100% for that segment. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that only a small percentage of the rice genome is recited in the claims of granted U.S. patents. The 300 kbp region with the highest percent coverage is chromosome 4, where one segment exhibits 3.55% patent coverage. For the entire rice genome, the percent coverage by granted U.S. patents is just 0.26%.

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U.S. Patent Applications: Number of Oryza sativa Sequences Referenced in Claims per Genome Segment

The blue bars in the plots below represent the number of sequences recited in the claims of U.S. patent applications that match a given 300 kilobase pair (kbp) segment of the rice genome. By match, we mean that the patent sequence is at least 150 base pairs in length and aligns with a rice genome sequence with a BLAST E value of 1e-200 or less. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

In contrast to the plots for the granted patents, these plots show that every segment of the rice genome matches 100 or more sequences recited in patent applications.

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U.S. Patent Applications: Number of Patent Applications that Claim Oryza sativa Sequences per Genome Segment

The blue bars in the plots below represent the number of U.S. patent applications that recite sequences in claims that match each 300 Kbp segment of the rice genome. By match, we mean that the patent sequence is at least 150 base pairs in length and aligns with a rice genome sequence with a BLAST E value of 1e-200 or less. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that for every 300 kbp segment of the rice genome, there are four or more patent applications that recite sequences in claims that match the rice genome.

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U.S. Patent Applications: Percent Coverage by Oryza sativa Patent Claims per Genome Segment

The blue bars in the plots below represent the percent of coverage of a given 300 kbp segment by U.S. patent applications. For example, if an entire 300 kbp segment matched sequences that were recited in claims US patent applications, the plot would read 100% for that segment. If there were multiple recited sequences matching the rice chromosome, only the highest scoring genome match was counted.

Summary of plots:

The plots show that a large percentage of the rice genome is recited in the claims of granted U.S. patents. Approximately 74% of the rice genome is recited in claims of U.S. patent applications.

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