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Biocceleration Releases GenCore 6.2, with Support for Percent Identity Searches and MPI based Parallelism

March 16, 2007 – Biocceleration Ltd. announced the release of GenCore 6.2, an updated version of its advanced sequence search acceleration system.

GenCore 6.2 offers the following new features and capabilities:

     -   A new Percent Identity Search algorithm, that is best suited for
intellectual property analysis. This algorithm calculates the best percent
identity between the query sequence and the database sequence, and reports the database sequences that achieved the highest percent identity score against the query.
     -    Using MPI based implementation, GenCore dynamic programming
search applications can now be parallelized over a cluster of Linux nodes. This enables running a single database search over a large number of Linux servers, thus providing orders of magnitude acceleration for computationally intensive searches.

These new capabilities are in addition to the already rich feature set
of GenCore 6:

-     A robust software package that runs on standard, general purpose computing and network architectures (Intel Pentium-4 or Opteron processor based systems or others), using Linux or other Unix operating systems.

-    Software based acceleration, using Biocceleration's highly optimized proprietary software implementation.

-    Up to 10-fold speed improvement relative to standard software implementations. More then 2 Billion Smith-Waterman Matrix cells calculations per second on a dual 3GHz P4 Linux machine. For detailed benchmarks see:

-    Support for a comprehensive set of search algorithms including Smith-Waterman (with affine scoring), ProfileSearch, ProfileScan, Translated Searches, Frame+, ProfileFrame+, HMMsearch, HMMscan, GeneWise

-    Seamless integration with a wide variety of DNA and protein database formats including FASTA, BLAST, GenBank, EMBL, SwissProt, GCG, NBRF, PIR, RAW, IG, PFAM (HMM)

-    Full user control over search parameters such as gap penalties, comparison tables, translation tables, scoring and normalization methods, and others.

-    Multi-query operation enables multiple sequences, or even a database subset, to be submitted as the search query set.

-    Multi-threaded operation enables full utilization of multiprocessor Unix/Linux machines.

-    Band, linear memory alignment algorithm for all search applications, produces fast, accurate alignment, even for very long sequences.

-    Support for multiple normalization methods enables customizing the software output for specific research projects.

With free download license for academic and research institutes, and reasonably priced license for commercial entities, Biocceleration enables existing Bioccelerator customers (BioXL/G, BioXL/P, BioXL/H), and new customers, easy upgrade to a new level of database search speed, performance, and flexibility.

For additional information, please visit Biocceleration’s products page at: http://www.biocceleration.com/Products.html
or contact us at info@biocceleration.com

Biocceleration Ltd. , a bioinformatics company, is the leading provider of systems and solutions for accelerating searches in protein and nucleic acids databases. Biocceleration provides software and hardware solutions that accelerate rigorous database search algorithms, like HMMsearch and Smith-Waterman by a factor of 10-1000 relative to general purpose servers. With install base of more then 50 biotech companies, pharmaceutical companies, and academic research institutes, Biocceleration offers a suite of hardware accelerators and software packages to support the industry needs for accelerated protein and DNA database searches.