Exciting, useful and newsworthy
Making the most of a sequence search – Sequence and keyword searching in USGENE
November, 2011
The number of patent documents with published sequence listings is constantly on the rise. Simple sequence searching more frequently results in large answer sets. This is especially true for sequences of high commercial interest and value which may be surrounded by heavy patenting activity. As a result, it becomes more important to include keyword search strategies comprising reasonable data content in addition to sequence searching. This search tip shows the unique feature on STN of combining a sequence search with additional sequence and patent publication related data for a more focused search strategy.
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e-Seminars
Two Dates: September 1, 2011 and September 20, 2011
Searching for siRNA and miRNA in STN patent databases. RNA interference (RNAi) is a system within cells that takes part in controlling which genes are active and how active they are. Two types of small RNA molecules, Micro RNA (miRNA) and Small Interfering RNA (siRNA), are central to RNAi. This e-Seminar will:
- Review indexing and patent classification search approaches for retrieving of siRNA and miRNA related records in CAplusSM and Derwent World Patents Index® (DWPISMSM)
- Use practical examples to provide advice for conducting effective sequence searches in USGENE®, GENESEQ™ (DGENE), PCTGEN and REGISTRYSM for these topics
This session will be of interest to novice and expert STN patent sequence searchers. Prior attendance or familiarity with the Sequence Basics and Multifile patent sequence searching e-Seminars is highly recommended (Recorded Events for both are available).
Link to presentation (PDF)
Performance improvements for USGENE sequence searches on STN
May 23, 2011
The performance of sequence searches in the USGENE database on STN has been enhanced. All search types - GETSEQ, GETSIM and BLAST - now run to completion in a fraction of the time previously experienced in the database on STN. These enhancements include upgrading the BLAST suite of programs in USGENE on STN to mpiBLAST 1.5.0.
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e-Seminars
Two Dates: May 17, 2011 and May 19, 2011
Sequence Basics. In this e-Seminar, learn how to most efficiently use the various sequence searching resources on STN. Topics will include:
- Introduction to STN sequence databases
- A review of recent enhancements
- BLAST search techniques
- Sequence Code Match (motif) search techniques
This session will be of interest to those learning STN sequence searching, and those who are experienced searchers, who would like a refresher and to keep up to date on the latest enhancements.
Link to presentation (PDF)
e-Seminars
Two Dates: July 7, 2011 and July 19, 2011
Multifile patent sequence searching on STN. This e-Seminar will focus on the theme of comprehensive multifile searching of patent sequence data, using USGENE, GENESEQ (DGENE), PCTGEN and REGISTRY databases on STN. The session will provide a variety of practical tips, from preparing the query through to post-processing search results into a final report using STN Express.
Link to presentation (PDF)
Patents and Pizza: USGENE on STN
February 8, 2011, 11:45 am - 1:00 pm
Improve your STN searching skills over lunch with a free STN Patents & Pizza session at the Embassy Suites Alexandria Old Town. Topics covered include USGENE database construction and content, timeliness, value-add/standardized search fields, search and display options, and the various ways sequence searching can be implemented in the database. Specific examples of Sequence Code Match searching will be discussed, including exact, amino acid family, and subsequence searching. Also, specific variability symbols will be used in a final Sequence Code Match search.
Link to presentation (PDF)
New USGENE STN Workshop Manual
May 19, 2010
A comprehensive new guide on USGENE content, features and STN searching is now available. The USGENE STN Workshop Manual provides thorough basic, intermediate and expert advice for every aspect of searching USGENE on STN. This includes step-by-step guidance on BLAST, FASTA and motif (fragment) searching, refining using text and date terms, and post-processing of search results using the STN Express Table Tool. The new guide is a must-have desktop reference for all USGENE searchers.
Download the USGENE STN Workshop Manual
STN Workshop
February 11, 2010
Boston, MA. USGENE is featured at the Sequence Searching on STN Workshop.
Link to workshop materials
PIUG Biotechnology Meeting
February 10, 2010
Cambridge, MA. SequenceBase Corporation sponsors the fourth annual PIUG Boston Biotechnology meeting, focused on patent sequence searching.
More about this meeting
Press Release
Dec 1, 2009
Japan Assoc. for International Chemical Information (JAICI) now markets in-house version of USGENE. Agreement gives the Japan Association for International Chemical Information (JAICI) the mandate to operate as SequenceBase Corp. marketing agent for subscriptions to USGENE in-house version and data available for customized subscription download.
Read the press release
New percent identity feature for sorting BLAST answer sets in USGENE on STN
November 30, 2009
A new sequence sorting feature for BLAST answer sets is now available in USGENE on STN. This new sorting option is a great support for reviewing large sequence answer sets and makes the identification of relevant sequences much more efficient and reliable. The enhanced sorting functionality allows you to sort a BLAST answer set according to local percent identity (IDENT). Additional sorting with this BLAST parameter is especially useful to identify short, highly similar sequences with a low over all BLAST similarity score. The new sorting feature is available for the results of all BLAST online, offline batch and Alert search options.
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Enhanced bibliographic and sequence information in USGENE
July 20, 2009
The USPTO Genetic Sequence Database (USGENE) now includes even more extensive bibliographic and text search options for refining U.S. patent sequence searches. USGENE sequence records now include:
- Priority application information, including priority application numbers (PRN) and dates (PRD)
- U.S. related application information, including U.S. related application numbers and dates
- Calculated patent expiration date (XPD) and patent term adjustment information (NTE, PTA) for issued patents
- A concise one-line Sequence Description (DESC), for improved efficiency when reviewing search results
On STN, the new data fields are all fully searchable and incorporated into the standard USGENE display formats BIB, BRIEF and ALL. In addition, the Sequence Description (DESC) field is now part of the free-of-charge TRIAL display format, for even faster relevance checking of USGENE search results.
Press Release
May 4, 2009
FIZ Karlsruhe now markets in-house version of USGENE®, the USPTO Genetic Sequences Database, in Europe. Agreement gives FIZ Karlsruhe the mandate to operate as SequenceBase Corporation’s marketing agent for USGENE® in-house version / USGENE® data available for customized subscription download / expert customer support.
Read the press release
Higher answer limits and a new HIT display format for USGENE on STN
May 3, 2009
Due to the increasing size of USGENE, the answer number limit for a Sequence
Code Match (SCM) GETSEQ search has been raised to 250,000 answers, and a new
free-of-charge HIT (synonym ALIGN) display format has been implemented on STN.
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