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How To Achieve Comprehensive, Faster, More Efficient IP Sequence Searching

How To Achieve Comprehensive, Faster, More Efficient IP Sequence Searching

How To Achieve Comprehensive, Faster, More Efficient IP Sequence Searching

Sep 28, 2021

Henk Heus
Blue test tube

Anyone who’s done an IP sequence search before can tell you it’s not easy. You need to cover all the relevant data, ensure you search the data in the right way and handle the results efficiently and effectively. Additionally, you want to keep it confidential. Failure to do all this can negatively impact results and conclusions, ultimately leading to flawed business decisions.

So, with this in mind, what steps can you take to prevent this happening?

Make Your Search as Comprehensive as Possible

The biggest challenge in IP sequence searching is finding a reliable, complete and up-to-date source of patent information. The IP sequence database you choose should include the more difficult-to-obtain countries, as well featuring sequences in tables and figures. For example, as of March 2021, the Lens contains about 375 million sequences, while GQ-Pat, Aptean GenomeQuest’s IP sequence database, contains 495 million sequences. So, an additional 120 million sequences.

In order to answer business-critical questions, you need to ensure you’re working with a complete source of information, one which is continuously updated with data streams from patent offices all over the world, as well as including the usable parts of databases like GenBank, EMBL and DDBJ.

Ensure You Search the Right Way

Needless to say, objective and repeatable search results are important in IP. Unfortunately, many popular sequence search algorithms are far from ideal for IP-related questions, with many preferring to use only a piece of the query sequence if it means they can report a higher percentage identity. Restricting the alignment length to a couple of residues will almost always produce 100% identity between any two sequences, but it doesn’t necessarily answer your specific query. Some of these solutions also don’t necessarily report all the alignments found, using a complicated statistical model that decides whether a match is significant or not. And, when the database grows, things that have been found in the past can disappear.

To overcome these issues, Aptean GenomeQuest developed and published the GenePast “percentage identity” algorithm. It aligns the entire query sequence while minimizing the number of mismatches, insertions and deletions. It doesn’t use a statistical model or algorithm shortcuts, and so always produces an objective and complete list of best possible results, regardless of database or alignment size.

Secure Hits To Answers Immediately

Too often, sequence search applications present outcomes as a long, static list of alignments making it difficult for you to filter out the relevant information. You might end up printing everything out, going through the hits one-by-one and looking up related patent information online, a workaround that’s time-consuming, error-prone and inflexible.

Instead, you need search outcomes presented as an interactive list, one which contains information about the alignments, the sequences and the related IP documents, including important dates, patent title, abstract, claims, assignee, classification and the legal status of a document. You can then group all alignments by patent number and patent family to see all related results together, with result analyses able to be adjusted and expanded at will. This allows you to get answers in minutes instead of days or weeks, enabling you to do more searches earlier in the product development cycle, as well as freeing-up search specialists and patent attorneys for other tasks.

Keep It Confidential

Confidentiality of IP searching is key, something that can’t be guaranteed with a public service. Choosing the right search solution will ensure all your data is handled and stored on a secure private network, with communication between your browser and the provider’s servers fully encrypted with password protection for your user account.

To achieve comprehensive, faster and more efficient IP sequence searching, you need an exhaustive and up-to-date database, using the right algorithms and parameters for the job and an efficient way to refine a list of search results into precise answers to your questions.

Over the last two decades, Aptean GenomeQuest has been used by many of the largest pharmaceutical, biotech and agricultural companies in the world, as well as specialized law firms and patent offices, to protect their IPs.

When it comes to protecting your IP, get in touch today to find out how Aptean GenomeQuest can help.

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