Protein sequence analysis software now accelerated
A
CLC bio product story
Edited by the Laboratorytalk editorial team
Jul 31, 2007
CLC Bioinformatics Cell uses SIMD technology to parallelise and thereby accelerate bioinformatics algorithms on Intel and AMD processor powered computers as well as computer clusters
At the 15th conference on Intelligent Systems for Molecular Biology (ISMB) and 6th European conference on Computational Biology (ECCB), this week in Vienna, CLC bio released an accelerated version of Sean Eddy's popular HMMER software suite for protein sequence analysis.
Senior scientific officer at CLC bio, Jannick Bendtsen, states: "Our implementation of HMMER runs on CLC Bioinformatics Cell, which uses innovative SIMD technology to unleash already existing powers in the computer processor to accelerate HMMER 25 times.
"Thus searches previously taking more than three hours can be done in less than ten minutes.
"This implementation works both with a graphical interface through our commercial workbenches, for example CLC Combined Workbench, or through a command-line interface - and it works on both Mac OS X, Windows and Linux".
With CLC Bioinformatics Cell users are able to utilise hidden computational powers in their computer or server.
The Bioinformatics Cell is optimised for Smith-Waterman searches, ClustalW alignments and HMMER protein sequence analyses.
Professor Ronald Worthington, pharmaceutical sciences at Southern Illinois University, previously stated: "One of the big things that genomics companies do is constantly screen the new data that's coming online to look for targets of interest using the HMMER software with the Pfam database - but it's really, really slow.
"Some Pfam searches we have done went on for weeks, even with dual-processor computers.
"If CLC bio can produce an SIMD-enabled HMMER, it will be huge for the genomics industry and academics".
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