Alignment is one of the basic operations in molecular biology to compare sequences. The most widely used methods for multiple sequence alignment include scalar-product based alignment of groups of sequences. We show that scalar-product based alignment algorithms can be significantly speeded up by generalpurpose computing on a modern commonly available graphics card. Thus the huge computational power of graphics cards can be exploited to develop high performance solutions for multiple sequence alignment.
Due to the increasing number of gates and the integration of hard-wired elements within Field Programmable Gate Arrays (FPGAs), high-level language programmability and tools become more necessary. Most of the existing approaches lack programming paradigms like parallelism or inclusion of predefined components to map algorithms to FPGAs efficiently. Other tools are difficult to handle because of their syntax or the way parallelism is integrated. In this paper we introduce the TransC language and focus on its concepts for concurrency as well as interprocess communication and synchronization with streams. TransC extends the C language by only a few keywords and hence eases the programming and porting of existing C-code in comparison to other approaches. A compiler is implemented that generates efficient VHDL code with only little overhead for programs with multiple processes.
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