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GenCore 6

Designed for Speed
GenCore 6 is a high-end software package for accelerated rigorous homology searches. GenCore 6 builds upon the proven strengths of Biocceleration's Bioccelerator, BioXL/P and BioXL/H, the industry standard in bioinformatics accelerators. Based on feedback from leading customers worldwide, and by using advanced proprietary technologies, Biocceleration developed GenCore 6 for higher throughput, and significantly improved price/performance ratio.

Major improvements of GenCore 6 over proprietary hardware accelerators include:

Two- to four-fold improvement in price/performance ratio.
Ability to run multiple search jobs in parallel (up to 32 jobs, depending on the computing hardware)
Runs on standard, general purpose computing and network architecture, like the Intel Pentium-4 processors or others, using Linux or other Unix operating systems.
Software based acceleration, using Biocceleration's highly optimized proprietary software implementation.

The enhanced performance provided by GenCore 6 enables the most sensitive and rigorous search algorithms to be used for timely queries against various DNA and protein databases. GenCore 6 accelerates rigorous search applications, such as Smith-Waterman, ProfileSearch, FrameSearch and HMMsearch, by a factor of 10 or more, relative to other commonly used software packages.

The HMMsearch, GeneWise and Frame+ Advantage
In addition to superior performance, GenCore 6 offers better biological modeling by implementing the advanced HMMsearch and GeneWise search applications, as well as Biocceleration's proprietary Frame+ algorithm.

HMMsearch and GeneWise, are improvements of the traditional ProfileSearch algorithm, that have become the industry standard for scanning nucleic or protein databases against known protein families or protein domains. GenCore 6 features an accurate, highly optimized, implementation of the HMMsearch algorithm and the GeneWise-9 algorithm.

Frame+, an improvement to FrameSearch, models frame shifts (usually caused by sequencing errors) and codon gaps independently and simultaneously. This sensitive application lets researchers reduce the number of false positive and false negative hits, thus obtaining more useful information with increased productivity.

Full Automation
GenCore 6 allows modular construction of multi-stage search strategies through a combination of unique automated features. The multi-query capability enables submission of several queries simultaneously. GenCore 6 automatically recognizes most popular database formats, thereby eliminating the need for database pre-processing. GenCore 6 provides a very flexible command line interface. Users can also utilize GenWeb - an intuitive, easy-to-use Web interface that provides innovative graphic output of search results.

Using general purpose computing hardware, the scalable GenCore 6 package offers the most advanced sequence analysis acceleration system available today.

Computing Hardware supported
Sun/Solaris, Intel compatible platforms running Linux, HP Alpha Tru64, and SGI/IRIX

Supported Configurations
2-128 processor servers on various SMP and/or cluster architectures (one search job per SMP server using multithreading)

Supported Search Algorithms
Smith-Waterman (with affine scoring)
ProfileSearch
ProfileScan
Frame+
ProfileFrame+
HMMsearch
HMMscan
GeneWise

Supported Data Formats
FASTA, BLAST, GenBank, EMBL, SwissProt, GCG, NBRF, PIR, RAW, IG, PFAM (HMM)

Interfaces
Web (HTML/Java) or Unix command line

Processing Speed
2-32 Billion Matrix Cell Updates per second, depending on the computing hardware.

Typical Benchmark
GenCore 6, running on an eight 3GHz Xeon processors Linux cluster, performs four Smith-Waterman (or ProfileSearch) search jobs against UniProt 4.2 using protein queries of 500 amino acids, in about 230 seconds