USGENE BLAST Search Portal

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Introduction

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 "all available peptide and nucleotide sequences from the published applications and issued patents of United States Patent and Trademark the Office (USPTO)."[1] The portal offers a "non-redundant version of USGENE®" that also includes "the complete archive of all USPTO 'mega' document sequences, and offers a full backfile of Patent Sequence Location (PSL), bibliographic and full-text details from 1981 to date."[1]


Major Recent Updates

December 2012

According to an email from a SequenceBase representative, the following enhancements have been added to the USGENE BLAST Search Portal:[2]

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.

According to an email from a SequenceBase representative, the following enhancement has been added to the USGENE BLAST Search Portal:[3]

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, Orbit.com, 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.


July 2012

According to an email from a SequenceBase representative, the following enhancements have been added to the USGENE BLAST Search Portal:[4]

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • USGENE record "Back to Projects" button - When you visit a USGENE BLAST Search Portal sequence record, there is now a button at the bottom allowing one-click navigation directly back to your Projects list.
  • Pricing flexibility - Optimization of pay-as-you-go functionality - The USGENE BLAST Search Portal supports a full unrestricted subscriber mode and a more restricted pay-as-you-go (PAYG) mode for those that need this pricing model. The PAYG mode has recently been optimized to make the workflow clearer and easier to navigate.
  • Our Privacy Policy has been added to the "Terms of use" page - We care about your privacy and our Privacy Policy is available via the Terms of use link, located at the bottom of the USGENE BLAST Search Portal interface.
  • Automated expiry emails - Seven (7) days prior to the expiry of your subscription, and again on the day of expiry, an automated notification email will inform you of your current subscription status.
  • About USGENE page - At the bottom of the USGENE BLAST Search Portal interface there is an About USGENE link. This page now provides the latest USGENE statistics, specifically sequence count and documents counts.


Use

After logging in, users can access four main tabs from the portal homepage:

  • Projects - Add a new project or open a current project. Within a project, users can search a nucleotide database using a nucleotide query. Users select a query sequence from a dropdown menu, enter a FASTA sequence (or upload the sequence from a file or a list of previously used sequences), select or enter any additional criteria or filters (subsequence range, low-complexity filter, algorithm parameters, and additional search options to limit the results by patent-related fields). User can view the results from each past search in the project by selecting the "view" option for a search in the "Project searches" list. The results page includes filtering options, the total number of each result type (sequences, redundant sequences, documents, and families), and a list of all sequences (which the user can expand to view related documents and patent families). Users can select document numbers to view the document record on Espacenet. Users select specific sequence records from the list to add to a list of selected documents for the project. The document list includes all documents related to the selected sequences. Users can choose documents from the list to generate a report, save the document list to Notepad, export the table to Excel, or add selected documents to the "My Patents" section.
  • My Patents - Users can add documents to the "My Patents" list by adding document results from a project, entering a patent ID to add to the list, or uploading patents from a file.
  • My Queries - Users can view a list of past queries from all projects.
  • Account - Users can change their profile and password.


Sources

  1. 1.0 1.1 "Welcome to SequenceBase and USGENE®." SequenceBase website, https://usgene.sequencebase.com/. Accessed March 21, 2012.
  2. "Latest USGENE BLAST Search Portal enhancements!" Email from SequenceBase representative. Received December 17, 2012.
  3. "Thomson Innovation full-text link options are now available in the USGENE BLAST Search Portal!" Email from SequenceBase representative. Received December 17, 2012.
  4. "Latest USGENE BLAST Search Portal Enhancements." Email from SequenceBase representative through the CHMINF-L listserv. Received July 12, 2012.

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