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Ten Mistakes to Avoid when Searching Gene Sequences
Avoid the costly pitfalls of inaccurate, irrelevant, and untimely search results - what you need to consider before your next search.
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You know you have searched the databases that are available. Work is getting done much faster and there is a greater confidence in the product we provide our client. 
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Solutions: GQ for IP - Biotech/Pharma
GenomeQuest provides patent and intellectual property professionals at biotech, pharma and life science research organizations with a complete do-it-yourself solution for centralized patent sequence search, powerful results analysis and reporting on a single-sequence or collections of sequences.
- Search in-house and GenomeQuest patent data sources simultaneously
- Filter down results from multiple sequence queries to those of relevance, in seconds
- Quickly organize your search results by patent, assignee or patent family
- Browse annotations with external links
- Generate detailed reports to view, print or share
Search Strategies
GenomeQuest provides a variety of algorithms for searching protein and nucleic acid sequences by homologies and/or similarity, including GenePAST (percent identity). The GenePAST algorithm is perfect for investigating claims on similar sequences specified in terms of percentage identity over the sequence. GenePAST is also ideal for short query sequences such as primers, probes or peptides. Users may also select the BLAST, Fragment Search, or Motif Search algorithm.
Keyword search enables users to find sequences using a keyword(s) located in the annotation. With GenomeQuest users can execute keyword searches using wildcards, proximity/phrase searching, as well as arbitrary combinations of And/Or phrases clauses (Available in September 2008 release).
Data Sources
For patent sequence searches, GenomeQuest includes the sequence patent database GQ-PAT. GQ-PAT delivers vital information including: Seq ID#, links to bibliographic information, patent family, legal status, patent sequence location, and more. GQ-PAT datasources include: USPTO, INPADOC/EPO, WIPO/PCT, and such public databases as GenBank, EMBL and DDBJ. GenomeQuest's continuous GQ-PAT database development project acquires, analyzes, and re-annotates new patent sequence information at a constant rate. GenomeQuest also includes the latest versions of GenBank, RefSeq, PDB, Uniprot, IPI, ENSEMBL, Ig Blast, and our premium database, DrugBank Pro.
| Country Code | Earliest Year of Document | No. of Documents | No. of Sequences |
|---|---|---|---|
| US | 1981 | 104,548 | 64,281,915 |
| WO | 1980 | 53,788 | 16,340,956 |
| EP | 1979 | 19,090 | 1,360,879 |
| JP | 1979 | 33,433 | 1,857,356 |
Results Analysis
Results analysis is a critical step to finding and organizing the information you really want. With GenomeQuest this can be accomplished in minutes instead of hours, even on multiple sequence queries, through a centralized Results page and flexible results table.
Filtering
Enabled by GenomeQuest’s FilterSmart technology users can quickly apply multiple parameters by which to narrow down multiple result sets. Easy-to-understand drop-down menus and text boxes, allow you to define alignment properties (%, length or position), dates, subject or query identifiers, or text filters such as Legal Status and many more.
Organizing Result Sets
In the results table, result sets from multiple queries are treated like a single result set so you can apply functions against all members simultaneously.
Grouping – Information can be grouped to view by Query, Subject, Alignment, Patent, Patent Family, Gene Name or Organism. Also control the number of visible best hits to be 1, 3, 5 or “all” results per group.
Changing your View – Quickly add or remove columns from the results display table to define the precise attributes to be viewed in the web page. You can then sort based on any of these columns.
Once you have defined the groups and columns, you can name and save the “View” to quickly apply to other sequence search results.
Reporting
With GenomeQuest, generating a concise Table (Excel) or Document (Word) report on your sequences of interest is easy. Full audit trails are included in all reports. GenomeQuest also includes special reports - Patent Number, and Patent Number plus Family list – to enable you to export this information for use in other search systems.
Accessing GenomeQuest
GenomeQuest uses a straightforward web-browser interface, so new and occasional users can do productive work right away. GQLive! is a secure, hosted GenomeQuest internet service. For enterprise users, GenomeQuest is available for on-site installation and includes GenomeCast, an automated data delivery service that always keeps your data up-to-date thereby eliminating sequence database maintenance chores.