The patent sequence database USGENE, providing all available peptide and nucleic acid sequences from the published applications and issued patents of the United States Patent and Trademark Office (USPTO), has been reloaded and enhanced on STNext.
In addition to faster search processing, the highlights of the new version of the USGENE are:
- New BLAST version and additional BLAST search options
- New FASTA version
- Expanded functionality for BLAST and GETSIM searches
- Better display of search results, New sorting option
- New search fields for the composition of nucleic acid and protein sequences
- Better compatibility with PATGENE and GENESEQ databases
- Better compatibility with full text patent databases
- Maximum number of hits increased
NEW BLAST VERSION AND ADDITIONAL BLAST SEARCH OPTIONS
USGENE now uses BLAST version 2.12.0. Four additional search options have been introduced, allowing for more precision in search results:
- /SQM - the megaBLAST algorithm, for searching highly similar nucleotide sequences
- /SQDM - the discontiguous megaBLAST algorithm, for searching similar nucleotide sequences but
allowing more mismatches
- /TSQP - the BLASTx algorithm, for searching nucleotide sequences translated from PATGENE protein
sequences
- /TSQNX - the tBLASTx algorithm, for searching translated nucleotides from PATGENE protein sequences
Additional details on these new search options can be found by typing HELP BLAST or HELP TLATION at an arrow prompt while in USGENE.
NEW FASTA VERSION
The FASTA algorithm, invoked by RUN GETSIM, has been updated to version 36.3.8h. It now allows searching of sequences up to 30K characters in length. The available search options are the same as before: /SQN for searching nucleotides sequences, /SQP for searching amino acid sequences, and /TSQP translating a nucleotide query in all six reading frames to an amino acid sequence and searching in the protein sequences. The display of the parameters, the overview diagram and the alignments are now the same for GETSIM and BLAST searches. Updated HELP information is available is available in HELP GSIM.
EXPANDED FUNCTIONALITY FOR BLAST AND GETSIM SEARCHES
For BLAST and GETSIM searches, answer sets can be generated in addition to the percentage score value of an alignment also with the percentage identity value of an alignment or a combination of both. See details in HELP BLAST or HELP GSIM.
IMPROVED USABILITY OF MOTIF SEARCHING (RUN GETSEQ) RESULTS
To improve the usability of Motif searching results, the entire answer set is now always included within a single L number. HELP GSEQ has been updated and includes additional information.
BETTER DISPLAY OF SEARCH RESULTS, NEW SORTING OPTION
New displays of similarity results are now available. For each BLAST or GETSIM search, two diagrams are now generated to provide an overview of the similarity between the retrieved sequences and the query:
- the number of answers, and
- a score for the specific degree of similarity for the search
For BLAST and GETSIM searches, L-numbers are each generated by entering ALL, an absolute score number, a score percentage, an identity percentage or a combination of the percentage. Each L-number can be used for further processing. While the default search results display is sorted by descending Accession Number, the ability to sort by descending Similarity Score (SORT SCORE D L1) has been retained and the ability to sort by descending Percent Identity (SORT IDENT D L1) has been introduced in USGENE. The capability to sort by Descending Percent Identity is now also being introduced in PATGENE and GENESEQ.
Alignments can be displayed for all three RUN options (BLAST, GETSIM, GETSEQ) as text with the display format ALIGN or as an image with ALIGNG.
NEW SEARCH FIELDS FOR THE COMPOSITION OF NUCLEIC ACID AND PROTEIN SEQUENCES
The introduction of new search fields reporting the nucleotide and amino acid composition of a specific sequence makes it possible to refine your searches to find sequences with a particular type of content. The new fields are as follows:
/AA - retrieves amino acid codes expressed as single characters
(see HELP AAC for the definitions of the amino acid codes)
/NA - retrieves the nucleotide codes (see HELP NUC)
/AA.CNT - retrieves the number of amino acids
/NA.CNT - retrieves the number of nucleotides
/AA.PER - retrieves the percentage of amino acids in the sequence
/NA.PER - retrieves the percentage of nucleotides in the sequence
Range searching is possible for the /AA.CNT, /NA.CNT, /AA.PER, and /NA.PER fields. Use the (S) proximity for precision searching results.
For example, nucleotides with high GC-content (Guanine, Cytosine) can be retrieved with:
=> S (G OR C)/NA (S) 60-100/NA.PER
BETTER COMPATIBILITY WITH THE PATGENE AND GENESEQ SEQUENCE DATABASES
While USGENE already had the Patent Sequence Location (/PSL) and Sequence Count (/SEQC) fields, their recent addition to PATGENE and GENESEQ means that the same sequence-specific searches can now beperformed in all three databases.
For every sequence in USGENE, the SHA-2 algorithm has been applied and indexed in the new field Sequence Key (/SEQK). The generated string (e.g., A0000030BD19782FC1774AF58E4CFFEE7F0E30588CBA14DCD38C), is specific to a sequence. Identical sequences receive the same string, regardless of the database of origin, or the organism from which the sequence was isolated. Further details on using the /SEQK field for efficient duplicate identification will be communicated in due course.
COMPATIBILITY WITH FULL TEXT PATENT DATABASES
Search fields common to the patent full text databases are now also available in USGENE:
/APO Application Number, Original
/DED Data Entry Date
/DUPD Data Update D
Most recent headlines
06/10/2025
France T l visions, France's leading broadcaster, has received the 2025 EBU ...
04/09/2025
Monumental Sports & Entertainment (MSE), in collaboration with Dalet, has been a...
07/08/2025
July 8 2025, 22:30 (PDT) Tata Motors & Dolby Bring Dolby Atmos to Harrier.ev, R...
15/07/2025
L3Harris put its CORVUS-RAVEN counter-small UAS capability into the hands of soldiers at VANAHEIM, showcasing its ability to provide passive signal detect, enha...
15/07/2025
Netflix Viewing Up 13.5% vs. May, Represents 42% of Monthly Gain for Streaming
...
15/07/2025
SAN FRANCISCO and BENGALARU, India Sangeeta Chakraborty has been named chief revenue officer at Amagi, a cloud-based software-as-a-service (SaaS) technology pro...
15/07/2025
As part of its mandate, the Advanced Television Systems Committee the U.S. organization tasked with developing advanced broadcast TV standards promotes ATSC 3.0...
15/07/2025
QuickLink, the leading global provider of multi-camera video productions and remote contributions, announces the launch of two innovative control panels Studi...
15/07/2025
Chris Kontopanos has joined leading high-quality microphone solutions manufacturer, DPA Microphones, as the company's new Regional Sales Manager for the Mid...
15/07/2025
Magnifi by VideoVerse, a global leader in AI-powered video automation, has launched a major platform upgrade built to simplify live and archival video editing f...
15/07/2025
Telestream, a global leader in media workflow technologies, will preview its latest innovations at IBC2025, Stand 7.B21. This year's showcase highlights how...
15/07/2025
IBC2025 is set to transform the onsite experience for its global attendees with the launch of a pioneering new feature: full integration of Amsterdam's GVB ...
15/07/2025
Music, sport and technology collided in spectacular fashion as ASB GlassFloor powered the debut of Beats N Buckets, Germany's first Basketball meets Hip-Ho...
15/07/2025
The Collectv, the Emmy award-winning broadcast solutions and workflows consultancy - and winner of Broadcast Tech's Team of the Year is delighted to announc...
15/07/2025
SipRadius, the expert in secure, low latency media transport, will showcase how broadcasters and media companies can take control of fragmented IP workflows at ...
15/07/2025
Appear, the global leader in live production technology, today announced its strategic partnership with beIN ASIA PACIFIC, a leading multi-platform sports media...
15/07/2025
Company marks 15 years of innovation at the show
Broadpeak, a leader in streaming and monetization at scale, will return to IBC (Hall 1, Stand F83. RAI, Amster...
15/07/2025
New software solutions extend trusted timing measurement across broadcast, venue, and professional AV applications
Hitomi Broadcast, the market leader in audi...
15/07/2025
SHENZHEN, China Telycam has added control options for its portfolio of pan-tilt-zoom (PTZ) cameras with a new plug-in for Elgato's Stream Deck family of con...
15/07/2025
MELVILLE, N.Y. Chyron said its Chyron LIVE cloud-native live production solution has successfully completed the Amazon Web Services (AWS) Foundational Technical...
15/07/2025
PHILADELPHIA The Xumo streaming platform joint venture between Comcast and Charter has announced the nationwide launch of a new line of Xumo TVs from Westinghou...
15/07/2025
LONGMONT, Colo. DPA Microphones said Chris Kontopanos has joined the microphone solutions provider as its new regional sales manager, Mid-Atlantic....
15/07/2025
NOT FOR DISTRIBUTION IN OR INTO OR TO ANY PERSON LOCATED OR RESIDENT IN THE UNIT...
15/07/2025
Harmonic's Hybrid, AI-Powered and Live Sports Streaming Innovations are Key ...
15/07/2025
The well-known and well-loved 4099 has been completely revamped. It features amazing CORE+ technology, which eliminates distortion and extends dynamic range, a ...
15/07/2025
Comscore Partners with HyphaMetrics to Launch Advanced Person-Level Audience Mea...
15/07/2025
Peak audiences of over half a million tune into both Kerry v Tyrone and Donegal ...
15/07/2025
PROTON Announces Production Facility Expansion Ahead of IBC2025 posted: 15/07/2025
Proton Announces Production Facility Expansion Ahead of IBC2025
Alongs...
15/07/2025
Submissions for NVIDIA's Plug and Play: Project G-Assist Plug-In Hackathon a...
14/07/2025
The Royal Moroccan Air Force hosted a C-130 award ceremony with L3Harris Technologies President of Intelligence, Surveillance and Reconnaissance Jason Lambert a...
14/07/2025
UK launch set for September, following on from recent US and Germany releases
London - UK, July 14, 2025 - Nielsen, a global leader in audience measurement, da...
14/07/2025
SHENZHEN, China Telycam has added control options for its portfolio of pan-tilt-zoom (PTZ) cameras with a new plug-in for Elgato's Stream Deck family of con...
14/07/2025
The awards are open to IBC2025 show exhibitors and offer a valuable platform for companies to raise awareness for the new products and solutions they will be la...
14/07/2025
Clear-Com is excited to announce a significant expansion of the award-winning Arcadia Central Station with new software updates. Together, these releases dram...
14/07/2025
Grass Valley and Daktronics today announced a strategic technology partnership that unites Grass Valley's live production expertise with Daktronics' lea...
14/07/2025
Cloud playout solutions provider, Veset, and swXtch.io, provider of cloud-based multicast and reliable networking solutions, are partnering to deliver multicast...
14/07/2025
Tintri , a DDN subsidiary and leader in AI-powered data management solutions, today announces a game-changing and award-winning refresh to its global Partner P...
14/07/2025
HighField AI, the broadcast industry's first agentic and multimodal AI platform for automating graphics production, is now commercially available. Developed...
14/07/2025
Encompass Digital Media has today announced that it has been delivering a complex global services project for DAZN, the world s leading sports entertainment pla...
14/07/2025
MASV (massive.io), the fastest, most reliable large file transfer platform trusted by over 10,000 global organizations, announced today it will showcase its nex...
14/07/2025
Calrec is introducing a series of usability, customisation and system enhancements across the entire range of Argo consoles at IBC 2025, on Stand 8.C47. Look ou...
14/07/2025
Fincons Group, IT business consultancy and systems integrator company with more than 40 years of experience in the market, is proud to announce a new engagement...
14/07/2025
Intinor returns to IBC to present the latest updates to its Direkt series. A key development on show is Intinor Direkt Management (IDM), a web-based interface f...
14/07/2025
This month, NVIDIA founder and CEO Jensen Huang promoted AI in both Washington, D.C. and Beijing - emphasizing the benefits that AI will bring to business and s...
14/07/2025
Sony's New Coach's Headset Was Designed in Collaboration With the NFL Featuring a custom dynamic boom mic, the headset will debut in the fall By Dan Da...
14/07/2025
Live From MLB All-Star 2025: MLB Network's Marc Caiafa and Tom Guidice on th...
14/07/2025
Back to All News
Netflix ISP Speed Index for June 2025
Product
14 July 2025
Global
Link copied to clipboard
One percent of Internet Service Providers (ISP...
14/07/2025
Back to All News
Netflix Begins Filming The Map of Longing With Al cia Falc , P...
The patent sequence database USGENE, providing all available peptide and nucleic acid sequences from the published applications and issued patents of the United States Patent and Trademark Office (USPTO), has been reloaded and enhanced on STNext. 
