Maximizing Efficiency: A Guide to Patent Sequence Extraction and Alignment

This workflow guide aims to provide a step-by-step approach to streamline the process of analyzing patent sequences using the powerful tools and features available in Patsnap's Analytics and Bio products. By following this guide, researchers and professionals can leverage the Sequence Assistant, Advanced Refinements, and Alignment tool to search for patents, extract relevant sequences, compare them, and align them with a reference sequence. Whether you are a biochemist, a biotech professional, or a patent analyst, this guide will equip you with the necessary tools and techniques to optimize your patent sequence analysis workflow.

Suppose we are interested in searching the patent space for all the patents that describe the discovery and subsequent engineering of an anti-CD3 epsilon antibody called SP34. The patent EP2982693A1 contains the murine SP34 sequence that was originally discovered and serves as the basis for several companies that humanize and further engineer it for therapeutic applications. Starting on the Analytics home page, proceed to the "Simple Search" section and input the patent number in the designated search field. Subsequently, the system will promptly display the desired patent, which can be accessed by clicking on it.

Once the patent is open in the new tab, use the "Sequence Assistant" to extract all the sequences into Bio by navigating to the "Seq Extraction" tab:

You will see a total of 16 sequences on the Bio Extraction page and navigate to the SP34 sequence which has the Seq Code 123556.

Check the checkbox next to the sequence and save it to the workspace by clicking "Save Sequence" in the pop-up. This will enable you to compare it with other sequences later.

I have created a new Workspace called SP34 and have saved the sequence to the "Test" folder:

Now click on the sequence code which will open up a new tab and then click on the "View in Analytics" button near the top of the screen.

Once you are on the Analytics results page, you can use the "Advanced Refinement" tool to further refine your results so that only patents that mention SP34 are shown. This tool is located near the top of the page next to the small search bar:

Select the TACD option and enter "SP34" which will bring down your results to 321 patents. You are welcome to further refine by additional keywords or even use the filters on the left-hand sidebar to make your search even more narrow and specific.

Once you are satisfied with your search refinements, choose the patents of interest by clicking the checkbox next to them. Then, select "Extract Sequences" from the appearing pop-up.

Once the sequences are extracted into Bio, you can further refine them by using the filters on the left-hand side. As an example, suppose we are interested in only Antibody sequences so we will select "Yes" under the "Antibody" filter and the number of sequences will go from 187 to 82:

Once you are happy with your refinements, save all the sequences to the initial workspace we created "SP34" in the "test" folder so that they can be compared with the first sequence we saved earlier. Please note that you can save 100 sequences at a time.

Open the workspace folder where the sequences were saved and navigate to the "Sequence" tab:

Select all the sequences (max up to 100 at a time) using the "Select all" option at the bottom of the page and then click on "Align Sequences" in the pop-up:

Once on the Alignment page, use the "Pair-Seq Alignment" option to align all the sequences with the SP34 sequence (Seq code 123556). You can choose any of the Alignment Algorithms from the drop-down list but for this workflow, we will go with BLAST:

After running the alignment, you will get the following report and you can save it by clicking on the blue "Save" button

These saved reports can be accessed from the homepage of Bio under the "Alignment Report" tab:

In summary, this workflow guide presents a practical and effective approach for analyzing patent sequences using the advanced tools and features offered by Patsnap's Analytics and Bio products. By following the outlined steps, researchers, patent analysts, and biotech professionals can capitalize on the Sequence Assistant, Advanced Refinements, and Alignment tool to seamlessly search, extract, compare, and align relevant sequences. By adopting this systematic methodology, users can increase efficiency, save time, and uncover valuable insights that contribute to advancements in therapeutic applications and research.