BioInfoMark: A Bioinformatic Benchmark Suite for Computer Architecture Research

The exponential growth in the amount of genomic data has spurred growing interest in large scale analysis of genetic information. Bioinformatics applications, which explore computational methods to allow researchers to sift through the massive biological data and extract useful information, are becoming increasingly important computer workloads. This paper presents BioInfoMark, a benchmark suite of representative bioinformatics applications to facilitate the design and evaluation of computer architectures for these emerging workloads. Currently, the BioInfoMark suite contains 14 highly popular bioinformatics tools and covers the major fields of study in computational biology such as sequence comparison, phylogenetic analysis, protein structure analysis, and molecular dynamics simulation. The BioInfoMark package includes benchmark source code, input datasets and information for compiling and using the benchmarks. To allow computer architecture researchers to run the BioInfoMark suite on several popular execution driven simulators, we provide pre-compiled little-endian Alpha ISA binaries and generated simulation points. The BioInfoMark package is freely available and can be downloaded from: http://www.ideal.ece.ufl.edu/BioInfoMark.

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