CLC Bioinformatics Cell - hardware-acceleration on your desktop

Do you know how many search results you are missing when using BLAST? Up to 50% of the hits are not found using BLAST. If you want 100% of the answers, and still want fast searches, you can improve the quality of your research by using the CLC Bioinformatics Cell.

The Cell includes the fastest Smith Waterman implementation ever made on standard hardware - nucleotide searches are accelerated up to 110 times and protein searches are accelerated up to 50 times on new computers.

White paper extract

In addition to documenting the Cells impressive speed-ups, the white paper elaborates on some important differences between Smith-Waterman based searches and BLAST searches:

  • BLAST is the better in the explorative phases of the research, and Smith Waterman is the better in the late stages of the research, where absolutely correct results are more important than estimates.
  • If you have query sequence data with too many of inherent errors, BLAST searches would often be so imprecise that the results are wrong or misleading.

Downloads

Product sheet

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US Letter

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User manual

A4

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Download white paper

If you're interested in the white paper, you can obtain it by clicking the "download" button below - and filling in the form. Once you have submitted the form, you will receive an email, giving you access to the white paper.

Version history

2.1 March 03 2008
• The Cell now supports computer clusters using MPI (command-line version only)
• Various bug-fixes
2.02 December 17 2007
• Fixed crash on very specific query sequences
2.01 October 4 2007
• Smith-Waterman calculations will not run into memory problems as easily; it can now only happen on machines with 4 cores on databases with extremely long sequences (100 Mb+)
• Smith-Waterman and HMMER will be faster on machines with 4 or more cores
• The Cell is now fully supported on Windows Vista
2.0 August 22 2007
• The Cell now runs an accelerated version of HMMer, with up to 37 times as fast searches as Sean Eddy's own implementation
• ClustalW now runs on multiple cores and now accelerates alignments up to 30 times
• Smith-Waterman BLAST searches have been optimized and now accelerates searches up to 144 times compared to Smith & Waterman's implementation
• Smith-Waterman BLAST searches have been improved on large amounts of data
• Web interface for all algorithms, providing easy access for multiple users
• Various bugs have been fixed
1.04 June 29 2007
• Plug-ins updated to be compatible with new release of the CLC Workbenches: CLC Combined Workbench 3.0, CLC DNA Workbench 3.0, CLC Protein Workbench 3.0, and CLC RNA Workbench 1.0
1.03 June 18 2007
• Implementation of possibility to see version number in command-line mode
• White papers updated, version 1.03
• Fix of smaller bugs
1.01 April 30 2007
• Now works on Intel-based Macs
• Fixed ClustalW bug at gaps longer than 200 nucleotides
0.94 April 2 2007
Added reward/penalty to parameters
0.93 March 12 2007
Changed names of executables
0.92 March 1 2007
Added database information to history.

 

 

 

With the Cell, you can speed up a Smith Waterman search previously taking 2 hours to around 1 minute, and the Cell thus removes the argument for using BLAST
With the Cell, you can speed up a Smith Waterman search previously taking 2 hours to around 1 minute, and the Cell thus removes the argument for using BLAST Visit clcbio.com Visit clcbio.com
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