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
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Xilinx®
FPGA (Field Programmable Gate Array)
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Available
Configurations
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XLH-4,
XLH-8, XLH-12, XLH-16, XLH-24, XLH-32 (the model number represents the
number of boards)
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Host
Support
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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
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100Base-T
network connection
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Applications
accelerated in Hardware
|
Smith-Waterman
(with affine scoring)
ProfileSearch
ProfileScan
Frame+
ProfileFrame+
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Supported
Data Formats
|
FASTA,
BLAST, GenBank, EMBL, SwissProt, GCG, NBRF, PIR, RAW, IG, PFAM (HMM)
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Interfaces
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Web
(HTML/Java) or Unix command line
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Processing
Speed
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3-24 Billion
Matrix Cell Updates per second, depending on the configuration
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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
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