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.

Benchmark

We have just released an accelerated implementation of profile HMM software for protein sequence analysis. It runs on CLC Bioinformatics Cell, which uses SIMD technology to unleash already existing powers in your computer processor. Searches previously taking more than 3 hours can be done in less than 10 minutes!

Hmmpfam

100 random sequences from Swiss-Prot were compared to the whole Pfam database. Both the fs and the ls versions of Pfam were used.

VersionTimeMCUPSSpeedup factor
Original1:19:2332,51 x
Cell0:03:26749,623,1 x

Hmmsearch

Ten random models from Pfam were compared to the whole of Swiss-Prot. Both fs and ls versions of the models were used.

VersionTimeMCUPSSpeedup factor
Original1:33:2357,11 x
Cell0:03:451420,324,9 x

 

Benchmark setup

Computer: 2.13 GHz Intel Core 2 Duo with 2 GB RAM running Fedora Core 6.

DatabaseHMMs/SequencesPositions
Swiss-Prot 53.3 274295100696439
100 proteins from Swiss-Prot10040993
Pfam 21.0 fs + ls179143772912
10 models from Pfam fs + ls203176

Notes
All programs were run with default parameters. Binary versions of the HMM files were used for hmmpfam.

 

 

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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