Updates to Sequence Searching in US Patents: 10 Changes to the USGENE® BLAST® Search Portal

[tweetmeme source=”Intellogist” only_single=false] We’ve taken a brief look at the USGENE® BLAST® Search Portal, a subscription online platform created by SequenceBase Corporation that gives users access to the USGENE® database.  Through the USGENE BLAST Search Portal, users can search for peptide and nucleotide sequences listed in US published applications and listed patents. An email from a SequenceBase representative recently outlined some of the major changes that the the search portal went through in July 2012, including updates to search, record viewing, filtering, and data export features.  Professional patent searchers, especially those specializing in the biotechnology field, will want to stay up-to-date on these changes to the official search portal for USGENE, which is a major resource for sequence data in US patent documents.

After the jump, we’ll review 10 major changes to search, viewing, filter, and export features on the USGENE BLAST Search Portal!

According to an email from a SequenceBase representative received in July 2012, the following enhancements have been added to the USGENE BLAST Search Portal:

  1. Improved search, display and reporting performance – The underlying USGENE database has been reorganized and optimized for faster search, display and reporting performance. For example, this includes all related documents being indexed into USGENE patent family groups, which are visible in the Evaluate table and Documents tab as “Family” numbers.
  2. Reorganization of BLAST algorithm parameters – The layout and defaults for BLAST “Algorithm parameters” have been adjusted to more closely reflect NCBI BLAST interface layout and defaults. This should make them a little easier to use and navigate. In-context help has also been added for each parameter.
  3. Latest BLAST version implemented – The latest version of NCBI BLAST is available (BLAST version 2.2.26). At any time the current version of BLAST can be confirmed in the About USGENE page, located at the bottom of the USGENE BLAST Search Portal interface. Please note that other services you may be using may not always provide the latest BLAST version.
  4. Automated naming of multiple uploaded sequence searches – To improve ease of use when uploading a series of FASTA format sequences for searching in the USGENE BLAST Search Portal, any search name you provide generates a simple series of numbered searches for the query sequences. For example, My protein query 1, My protein query 2, etc.
  5. Three additional filters in the Evaluate table
    • Database filter – Only show sequence hits from either granted (issued) patents, or published patent applications.
    • Sequence count filter – Only show sequence hits from documents with a total sequence count below a chosen value.
    • My patents filter – Only show sequence hits from documents which are in My Patents.
  6. Profile option for Evaluate table in Expand all view – In the Account tab, “Edit profile” section, you can now set your preference to initially see “Evaluate table” results in either condensed “Collapse all” (default) or detailed “Expand all” view.
  7. Generate report in .DOCX format – The Documents tab now has the option to generate a detailed report in the .DOCX format in addition to the PDF format. The main advantage of the .DOCX format is that it can be more easily edited and customized before sharing with your colleagues. The structure and content of this report is based directly on the feedback we have received from customers.
  8. Generate table option – The Documents tab Generate table option creates a .XLS tabular report of results. The table is organized based on sequence hits, and includes a standard combination of data fields relating to the sequence hits. The structure and content of this table is based directly on the feedback we have received from customers.
  9. USGENE record browse buttons – When you open a USGENE BLAST Search Portal sequence record, there are now two sets of browse buttons at the top. The “Sequence number” browse buttons allow you to navigate between sequence records from an individual document, and the “Sequence key” buttons allow you to navigate between identical sequence records from different documents.
  10. USGENE record links to legal status and patent families – When you click on “More” publication information in a USGENE BLAST Search Portal record, two “Further information” links are now available. “Legal Status” takes you to current Espacenet legal status, and “Patent Family” takes you to current international patent family information available at Espacenet.

The Evaluate tab on the USGENE BLAST Search Portal, which now lists Family numbers (image from screenshot on Blast Search Portal website).


The updates to the US GENE BLAST Search Portal improve every step to the search process, from the reorganization and new help features on BLAST algorithm parameters to the new  export options under the Document tabs.  The addition of more filtering options under the Evaluate table improves the user’s ability to quickly narrow the dataset based on specific criteria, such as the publication status or the sequence count. The linking of Espacenet legal status and family data to the USGENE records directs users to additional freely available  information related to relevant US patent documents.  Overall, I’d recommend that patent searchers who regularly use sequence searches should sign up for the USGENE BLAST Search Portal’s 30 day free trial to test the new search, view, filter, and export features.

What do you think of the recent updates to US GENE BLAST Search Portal? Let us know in the comments!

Patent Searches from Landon IP

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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