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BioXL/H

Designed for Speed

BioXL/H is a high-end hardware accelerator for rigorous homology searches. BioXL/H builds upon the proven strengths of Compugen's Bioccelerator and BioXL/P, the industry standard in bioinformatics accelerators. Based on feedback from leading customers worldwide, Compugen designed the BioXL/H for higher throughput.

Major improvements over the BioXL/P include:

  • Twice the number of processing units per board for significant search speed-up.
  • Three fold improvement in size and speed of the internal cache disk, which allows for storing considerably larger databases in internal cache thus providing additional improvement in throughput and reducing the need for data transfers across the network.
  • Standard network interface and open Linux-based operating system for smooth integration into local network.
BioXL/H's enhanced performance enables the most sensitive and rigorous search algorithms to be used for timely queries against various DNA and protein databases. BioXL/H accelerates rigorous search applications, such as Smith-Waterman, ProfileSearch, FrameSearch and HMM, by a factor of 100-1000.

The HMM and Frame+ Advantage
In addition to superior performance, BioXL/H offers better biological modeling by implementing Compugen's proprietary Frame+ algorithm as well as the public domain HMM and GeneWise search applications.

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.

The BioXL/H also enables database searches that use PFAM HMMs either as a query or as a database.

Full Automation
BioXL/H's sequence analysis software, GenCore, 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 automatically recognizes most popular database formats, thereby eliminating the need for database pre-processing. GenCore 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.

Combining superior throughput and computational power, the scaleable BioXL/H system, teamed with GenCore and GenWeb, offers the most advanced sequence analysis acceleration available today.


Hardware Processing Technology
Xilinx FPGA (Field Programmable Gate Array)
Available Configurations
XLH-4, XLH-8, XLH-12, XLH-16, XLH-24, XLH-32 (the model number represents the number of boards)
Host Support
SUN Solaris, Intel compatible platforms running Linux, Compaq Alpha Tru64, and SGI IRIX
* Large BioXL/H systems (BioXL/H-16 or higher) are supplied with a pre-installed dual CPU Linux host server, for improved compatibility and performance.
Connection Type
100Base-T network connection
Applications accelerated in Hardware
Smith-Waterman (with affine scoring)
ProfileSearch
ProfileScan
Frame+
ProfileFrame+
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
3-24 Billion Matrix Cell Updates per second, depending on the configuration
Typical Benchmark
XLH-8 performs a Frame+ search against SwissProt 36 using a two-strand nucleic query of 500 bases in length in 17 seconds
Environmental
Environmental Specifications