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 Extension module), for topics such as drug targeting, next-generation sequence data analysis and patent landscape analysis.
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GenomeQuest High Throughput Extension

GenomeQuest High Throughput Extension (GQ HTx) is a component of our High Throughput Module, and enables users of GenomeQuest to access and utilize all the high-throughput, high-performance computing functions of a bioinformatics facility without the burden, through simple command-line workflows. Analyze 10's to 10,000's of sequence queries at once, access aggregated content from in-house and GenomeQuest data resources, and develop workflows, all from your desktop.

Effortless High Throughput Workflows

GenomeQuest HTx unables users to script sequence analysis workflows from their desktop (view Sample Workflows), without worrying about mundane details of sequence database management and administration, or about hardware contraints. Requiring only an Internet/Intranet connection, GQ HTx transforms your desktop into a high throughput bio-computer for such work as: checking on new annotations of sequences showing interesting transcriptional profiles, checking for patents containing specific families belonging to a competitor ( or partner), creating and maintaining sequence repositories of arbitrary definition, providing computational support for humanizing antibody sequences.

Straightforward Sequence Information Management

While the easy-to-use web interface of GenomeQuest empowers bioinformaticians to serve their user community, GQ HTx provides them with sequence analysis abilities of their own use. Using simple command structure (gqfetch, gqsearch, gqresults), GQ HTx alleviates the complexitities of scripting while enabling users to:

Search and fetch sequences on the basis of indentifiers or other key words in the annotation.

create and manipuate virtual databases on GenomeQuest as combinations of subsets of public databases.

Launch large sequence searches through full specification of search algorithms and parameters.

Manage large search processes including checking search progress, interupting jobs and assigning access to other users.

Publish any results in the GenomeQuest web application.

Filter results on the basis of alignment and annotation properties using FilterSmart technology.

GQ HTx Configuration

GenomeQuest HTx is a Java client program that can reside on a Unix or Linux desktop. GQ HTx can be configured to use GenomeQuestLive! which provides you instant access to the underlying high performance computing platform through a secure connection. Alternately, it can be configured to run on your own GenomeQuest Applicance, enabling you to keep all sequence work behing the firewall. Either way, all GenomeQuest users access the same continually-updated set of databases.