Resources
Bioinformatics for High- Throughput Sequence Search and Analysis White Paper
Through example, GenomeQuest will demonstrate how users can access its high throughput capabilities from the web interface or command-line (using GenomeQuest High Throughput Module), for topics such as drug targeting, next-generation sequence data analysis and patent landscape analysis.
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Solutions: GQ for Bioligical Sequence Analysis
For researchers, bench scientists and informatics professionals, GenomeQuest provides rapid and relevant answers to your research questions using virtualized bioinformatics tools on your desktop.
- Browse in-house and GenomeQuest databases by keyword and BLAST 1, 1,000, or 100,000 of selected sequences
- Group, classify and count results by gene, organism or other attributes
- Annotate lists of genes and ID's from micro array experiments and generate reports
- Export selected sequence records and launch third party sequence analysis programs such as PFAM or Vector NTI
The GenomeQuest High Throughput Platform
GenomeQuest gives you all the functionality of a bioinformatics facility including sequence search, algorithms, results analysis and management and more without the need to worry about hardware constraints, sequence database management, or administration. The GenomeQuest platform provides virtual access to these functions, from any desktop via the GQ High Throughput Module which enables power-users to work from the command-line to execute high-performance workflows, performed directly on the GQ server.
Data Sources
GenomeQuest provides a platform for accessing aggregated in-house, public and commercial sequence data, enabling users to run database searches from a centralized platform. GenomeQuest includes the latest versions of GenBank, RefSeq, Uniprot, IPI, and ENSEMBL among others, and our premium database, DrugBank Pro. GenomeQuest also houses the largest, annotated patent sequence database, GQ-PAT.
Search Strategies
GenomeQuest provides a variety of search algorithms for protein and nucleic acid sequence homologies and similarities including BLAST, Percent Identity(GenePAST), Fragment search and Motif search.
GenomeQuest also offers keyword search capabilities. Select protein or nucleic databases through checkboxes on the user interface or through specifying an identifier on the command line. Results can be narrowed down by filtering on default fields within the annotation as well as exported to a Word or Excel report. GenomeQuest offers wildcards, proximity/phrase searching, as well as arbitrary combinations of And/Or clauses (available Sept. 2008).
Results Analysis
Results analysis is a critical step to finding, organizing and understanding the information at hand. With GenomeQuest this can be accomplished in minutes instead of hours, even on multiple sequence queries. With GenomeQuest's central Results page, and flexible results table you can analyze, and re-organize your results for best comprehension using a variety of functions including:
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 filter by organism, gene name, even by a keyword located in the description: name of protein family equals "kinase".
Grouping
Information can be grouped to view by Query, Subject, Alignment, Gene Name or Organism to see the diversity of results from different angles. 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.
Exporting Sequences
GenomeQuest enables you to export results in a variety of formats to third party applications e.g. Clustalw, Vector NTI or others which may or may not be native to GenomeQuest. Enterprise users can add-on their own sequence analysis applications.
Accessing GenomeQuest
GenomeQuest is designed to be used by individuals with direct and immediate needs for sequence information. 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, through-the-firewall service that eliminates sequence database maintenance chores.
For Bioinformatiticians looking to serve their user community, GenomeQuest provides the GenomeQuest High Throughput Module where you can script powerful workflows directly from your desktop, without the IT burden.