SUMMARY: : Similarity searches of amino acid sequences against the public metagenomic data can provide users insights about the function of sequences based on the environmental distribution of similar sequences. However, a considerable reduction in the amount of data or the accuracy of the result was necessary to conduct sequence similarity searches against public metagenomic data, because of the vast data size more than Terabytes. Here, we present an ultra-fast service for the highly accurate amino acid sequence similarity search, called PZLAST, which can search the user's amino acid sequences to several Terabytes of public metagenomic sequences in ∼10-20 min. PZLAST accomplishes its search speed by using PEZY-SC2, which is a Multiple Instruction Multiple Data many-core processor. Results of PZLAST are summarized by the ontology-based environmental distribution of similar sequences. PZLAST can be used to predict the function of sequences and mine for homologs of functionally important gene sequences. AVAILABILITY AND IMPLEMENTATION: PZLAST is freely accessible at https://pzlast.riken.jp/meta without requiring registration. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

We have achieved a sustained calculation speed of 281 Tflops for the optimization of the 3-D structures of proteins from the X-ray experimental data by the Genetic Algorithm - Direct Space (GA-DS) method. In this calculation we used MDGRAPE-3, special-purpose computer for molecular simulations, with the peak performance of 752 Tflops. In the GA-DS method, a set of selected parameters which define the crystal structures of proteins is optimized by the Genetic Algorithm. As a criterion to estimate the model parameters, we used the reliability factor R1 which indicates the statistical difference between the calculated and the measured diffraction data. To evaluate this factor it is necessary to reconstruct the diffraction patterns of the model structures every time the model is updated. Therefore, in this method the nonequispaced Discrete Fourier Transformation (DFT) used to calculate the diffraction patterns dominates most of the computation time. To accelerate DFT calculations, we used the special-purpose computer, MDGRAPE-3. A molecule, Carbamoyl-Phosphate Synthetase was investigated. The final reliability factors were much smaller than the typical values obtained in other methods such as the Molecular Replacement (MR) method. Our results successfully demonstrate that high-performance computing with GA-DS method on special-purpose computers is effective for the structure determination of biological molecules and the method has a potential to be widely used in near future.

We performed molecular dynamics (MD) simulation of 9 million pairs of NaCl ions with the Ewald summation and obtained a calculation speed of 1.34 Tflops. In this calculation we used a special-purpose computer, MDM, which we are developing for the calculations of the Coulomb and van der Waals forces. The MDM enabled us to perform large scale MD simulations without truncating the Coulomb force. It is composed of WINE-2, MDGRAPE-2 and a host computer. WINE-2 accelerates the calculation for wavenumber-space part of the Coulomb force, while MDGRAPE-2 accelerates the calculation for real-space part of the Coulomb and van der Waals forces. The host computer performs other calculations. We performed MD simulation with the early version of the MDM system: 45 Tflops of WINE-2 and 1 Tflops of MDGRAPE-2. The peak performance of the final MDM system will reach 75 Tflops in total by the end of the year 2000.

We describe the GRAPE-4 (Gravity Pipe 4) system, a special-purpose computer for astrophysical N-body simulations. In N-body simulations, most of the computing time is spent to calculate the force between particles, since the number of interactions is proportional to the square of the number of particles. For many problems the accuracy of fast algorithms such as the particle-mesh scheme is not sufficient and we have to use the straightforward direct summation. In order to accelerate the force calculation, we have developed a series of hardware, the GRAPE (Gravity Pipe) systems. The basic idea of our GRAPE systems is to develop a hardware specialized for the force calculation. The rest of the calculation is performed on the general-purpose computer connected to GRAPE. The GRAPE-4 system is our newest hardware, scheduled to be completed in early 1995. Planned peak speed is 1.15 Tflops. This speed is achieved by running 1920 pipeline LSIs, each provides 600 Mflops, in parallel. A prototype system has been completed July 1994, and the full system is now under manufacturing.>

GRAPE (GRAvity PipE) is a special-purpose computer designed to accelerate the numerical integration of the astrophysical N-body problem. The prototype hardware, GRAPE-1, is designed as the backend processor that calculates the gravitational interaction between particles. All other calculations are performed on the host computer connected to GRAPE-1. For large-N calculations (N>or approximately=10/sup 4/), GRAPE-1 achieves about 200 Mflops equivalent in one board of the size of about 40 cm by 30 cm, consuming 2.5 W of power. The specialized pipelined architecture of the GRAPE-1 optimized for the large N calculation is the key to the high performance. The authors describe the design, construction and programming of GRAPE-1. The architecture is quite simple, and it is easy to put one pipeline into one LSI chip and make many pipelines work in parallel, without creating a communication bottleneck.>