News | News By Subject | News by Disease News By Date | Search News
Get Our FREE
Industry eNewsletter

Paracel Announces AGENT 2.0 At Bio-IT World Conference And Expo

10/19/2005 5:10:40 PM

Improved Algorithms and Editing Tools Accelerate Genotyping and Mutation/SNP Discovery

BOSTON--(BUSINESS WIRE)--March 31, 2004--Paracel, Inc.®, a business unit of the Celera Genomics Group of Applera Corporation and a leading provider of Applied High Performance Computing(TM) solutions, today announced the availability of version 2.0 of AGENT(TM) intended for use in research labs. AGENT, Paracel's Automated GENotyping Tool, is software that has been developed to accelerate and streamline the genotyping and mutation discovery process by incorporating technology that accurately handles the intricacies of trace file datasets. Paracel will be featuring AGENT and its integrated systems for life sciences at Booth #606 at Bio-IT World Conference and Expo, March 30-April 1, 2004 ( The HLA region of the human genome and viruses such as HIV typically display high degrees of sequence complexity due to their high mutation rates. A common bottleneck of the direct DNA sequencing method is the analysis of sequence data, a process that can be both time consuming and error prone.

"The accurate sequencing of viral genomes, including quasi-species and other heterogeneous data, requires the capability to detect multiple peaks in any location and distinguish true secondary peaks from noise. AGENT incorporates algorithms to take into account the challenges of these datasets to produce accurate results," said Cecilie Boysen, senior scientist at Paracel.

Accurate Sequence-Based Genotyping

AGENT incorporates Paracel's advanced TraceTuner(TM) MX base calling and quality value assignment algorithms. TraceTuner MX has been optimized for heterozygous and mixed bases and is able to distinguish between noise peaks and even low-level mixed bases seen in pooled samples and in viral samples such as HIV. TraceTuner MX can read through dye blobs, and is often able to identify mixed bases inside the dye blobs.

AGENT employs advanced automated assembly and consensus calling algorithms that make full use of mixed base calls and assigned quality values. This exhaustive data handling yields highly accurate consensus sequences, even when the underlying base calls do not agree.

Automated Sample Processing and Simplified Review

Labs are responsible for tracking large volumes of samples and for reviewing and editing the results. AGENT enables users to easily track and navigate between patient samples through convenient graphical user interfaces that increase user productivity. The new multiple patient alignment feature for reviewing the consensus sequences and mutation lists of multiple patients provides a convenient way to screen for consistent sequencing errors and emerging mutation patterns as chromatograms from different samples can be displayed together for direct comparison.

"As a high-throughput SNP and mutation discovery service, we rely on software that can provide the necessary accuracy in a timely manner. AGENT 2.0 with the new multiple patient feature will greatly improve our production," said Nicole Gordon, lab manager for Polymorphic DNA.

In addition, AGENT assigns quality values to the consensus sequence calls, which enables users to easily identify the areas that require more analysis. This results in decreased editing time and facilitates the detection of false negatives.

Technical Specifications

AGENT is built upon a client/server architecture. Server platforms include OSF1 V4.0f for Compaq Alpha EV6, Solaris 2.6 for SPARC, Solaris 2.7 for x86 and RedHat Linux 7.1 for x86. Paracel can deliver AGENT as an integrated system, pre-configured to run on a Paracel Cyclone Linux server. The AGENTView client GUI runs on Windows 2000 and Mac OS X. AGENT is available immediately.

About Paracel, Inc.

Paracel is a leading provider of Applied High Performance Computing solutions to solve the most technically challenging problems. Founded in 1992 to commercialize high-volume data analysis technology, Paracel today is a premier provider of integrated turnkey systems and software for over 500 customers worldwide. Paracel is headquartered in Pasadena, Calif., and is a wholly owned subsidiary of Celera Genomics.

(C) AGENT and Paracel are trademarks and registered trademarks of Paracel, Inc. All others trademarks are property of their respective owners.

-------------------------------------------------------------------------------- Contact:

Paracel, Inc.

Amanda Sheldon, 626-744-2086


Source: Paracel, Inc.

Read at

comments powered by Disqus