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  • News & Commentary - Message forums

    Software: GPU-HMMer announced
    Submitted by Joe Landman; posted on Tuesday, February 10, 2009

    Scalable Informatics (, provider of high performance computing and storage solutions, in cooperation with researchers at the University at Buffalo, announced the introduction of GPU-HMMER, an NVIDIA CUDA implementation and extension of MPI-HMMER. GPU-HMMER and MPI-HMMER are open-source implementations of the HMMER protein sequence analysis suite that profoundly reduce computation times.

    The MPI-HMMER implementation capitalizes on the computational power of multiple processors on large clusters, whereas GPU-HMMER is designed to leverage NVIDIA GPUs (graphics processing units) to accelerate processing on computing systems. Performance of up to 100x faster than a single core of AMD Shanghai 2.3 GHz has been measured for 3 GPU units.


    HMMer, GPU-HMMer, and mpiHMMer are all GPL v2 licensed. This work is based upon the 2.3.2 version of HMMer. Version 3.0 of HMMer is in alpha at


    See[...]nced/ for some details, and the mpiHMMer site for downloads, documentation, support, etc.

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