Important Changes to Patent Sequence Search Tools

Major updates have been added on two of the largest search platforms for locating peptide and nucleic acid sequences within patent records, and Intellogist is here to bring you all the details on these recent changes to to the coverage, search, and display features on GenomeQuest and the USGENE BLAST Search Portal. GenomeQuest is a biological sequence data management platform created by GenomeQuest, Inc., and GenomeQuest maintains its own patent sequence database, GQ-PAT. Many other non-patent data files are also simultaneously searchable on the platform, such as GenBank, RefSeq, Swiss-Prot, and other NCBI and EBI files.  We last highlighted the Chinese patent office sequence data added to GenomeQuest in 2010, and today we’ll look at additional India, Brazil, and Chinese patent sequence data now available in an Emerging Countries Domestic Patents Archive.  Additional GenomeQuest updates include normalized patent assignee names and subject database filtering.

The USGENE® BLAST® Search Portal is a subscription-based online search platform created by the SequenceBase Corporation that allows users to search USGENE®, a database that lists peptide and nucleotide sequences from US published applications and issued patents. Previously in July 2012, there were a number of updates added to the portal, and additional updates were implemented in December 2012, including options to expand and download all alignments for search results.

Continue reading to learn about all the new coverage, search, display, and download options recently added on two major sequence search platforms, GenomeQuest and the USGENE BLAST Search Portal!

GenomeQuest Updates

October 2012, Emerging Countries Domestic Patents Archive:

According to a GQ-PAT Premium Update Sheet from GenomeQuest, GQ-PAT Premium now offers an Emerging Countries Domestic Patents Archive that covers “domestic-only filed applications/patents with sequences from China, Brazil, India and an expanding list of counties”:

  • India: GQ has identified and acquired hundreds of India patents with sequences. These are being curated and formatted. We currently have 260 of these domestic-only filed Indian patents with sequences and will only continue to add going forward. By November, we expect to have an additional 800 Indian patents available through GQ-PAT Premium.
  • Brazil: There are over 270 Brazil patents in GQ-PAT Premium. This brings us up to date with all domestic only Brazil patents with sequences. We will continue to add new Brazil patents with sequences moving forward.
  • China: We have made strides to bring new China patents with sequences into GQ-PAT Premium faster. We believe we have the industry’s fastest delivery of sequence-based patents from the China patent office (SIPO).

The next countries under consideration to add to the archive include “Argentina, South Africa, Canada, Australia, Vietnam, Russia, European Countries (patents with no EP), Mexico, Taiwan, Indonesia, Philippines, Vietnam, Chile, and Malaysia.”

October 2012, Extended Legal Statuses:

According to a GQ-PAT Premium Update Sheet from GenomeQuest, extended legal statuses are now available on GQ-PAT Premium, and “these legal statuses are not limited to Premium content, but are only accessible to Premium customers.” The update sheet gives the following description of the extended legal status:

When doing searches for patents using GenomeQuest’s premier IP product, you will be able to view legal statuses beyond Granted and Application. Legal Statuses will include: Pending, Granted, Lapsed, Expired, and Revoked and are updated monthly, presenting the most current and up to date information available.

For more information on viewing the Extended Legal Status and Legal Status National Phase (which will only be available to users that subscribe to GQ-PAT Gold+ or GQ-PAT Platinum after January 2013), see this page on the GenomeQuest Documentation Wiki.

January 2013, Normalized Patent Assignee and Subject Database Filtering:

According to a GenomeQuest representative, the following updates have been added to the system:

  • Normalized Patent Assignee: Allows you to group and filter so you can quickly find or remove the correct patent holders. This feature is only available to Gold Plus & Platinum subscribers. See this page on the GenomeQuest Documentation Wiki for more information on the Normalized Patent Assignee.
  • Subject database filtering: Now when you are searching, you can filter based on either publication date and/or remove the jumbo sequences to narrow your results which will return more relevant hits. See this page on the GenomeQuest Documentation Wiki for more information on Subject Databases Prefiltering.
New GenomeQuest fsubject database filtering options (screenshot from GenomeQuest promotional email).

New GenomeQuest subject database filtering options (screenshot from GenomeQuest Documentation Wiki).

USGENE BLAST Search Portal Updates

December 2012, Expand/Download All Alignments:

According to an email from a SequenceBase representative:

Over the last few weeks two important detailed enhancements have been made to the USGENE BLAST Search Portal Evaluate tab results table. We invite you to try out the new features and let us know what you think about them. The enhanced features are summarized below.

  • Expand all alignments: At the top right of the Evaluate tab results table there are now two Expand all options. A completely new option to Expand all alignments, and the previously existing one to Expand all documents. The two options now work seamlessly together to allow you to see all the alignment details, and/or all bibliographic summary information for the hit sequences, in one step.
  • Download all alignments: At the top left of the Evaluate tab results table there are now three buttons: Add all selected, Add all with filter applied, and Download alignments. The new Download alignments button will export a plain text file of all the alignments, intended for use in offline expert analysis of the BLAST search results.
"Expand all alignments" option beside each search result on the USGENE BLAST Search Portal (image from SequenceBase email)..

“Expand all alignments” option beside each result on the USGENE BLAST Search Portal (image from SequenceBase email).

December 2012, Links to Thomson Innovation Records:

According to an email from a SequenceBase representative:

SequenceBase are pleased to announce that the USGENE BLAST Search Portal now provides the option to set patent and published application number full-text links to go directly to corresponding Thomson Innovation records. To change the default USGENE BLAST Search Portal full-text links to go to Thomson Innovation, simply visit the “Edit profile” section of the Account tab and select your preferred service. In addition to Thomson Innovation, your full-text link options include PatBase Express,, and Espacenet. Changing the default setting will update the default full-text links throughout the USGENE BLAST Search Portal, including in any subsequently generated reports in either XLS, DOCX or PDF format.


New coverage, such as the Emerging Countries Domestic Patents Archive on GenomeQuest, and updated search and display features, such as the options to expand/download all alignments for a result on the USGENE BLAST Search Portal, are regularly added to these two subscription-based sequence searching platforms.  Professional patent searchers, especially those who conduct searches for new innovations in the biotech and pharmacology fields, need to stay updated on the best search methods and coverage availability for peptide and nucleic acid sequence data within patent documents.  Continue to check the Intellogist Community Reports for GenomeQuest and the USGENE BLAST Search Portal to learn about  further updates on search, display, and coverage changes for these two major patent sequence search tools.

Have you recently used either GenomeQuest or the USGENE BLAST Search Portal to conduct sequence searches within patent records?  Let us know how you feel these patent sequence search portals compare to each other in the comments!

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This post was contributed by Joelle Mornini. The Intellogist blog is provided for free by Intellogist’s parent company Landon IP, a major provider of patent searches, trademark searches, technical translations, and information retrieval services.

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