Hybrid Architecture for Accelerating DNA Codeword Library Searching

-- A large and reliable DNA codeword library is the key to the success of DNA based computing. Searching for the set of reliable DNA codewords is an NP-hard problem, which can take days on the state-of-art high performance cluster computers. This work presents a hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA reverse complement, edit distance codes. Two applications of this architecture were implemented and evaluated, including a code generator that uses a genetic algorithm (GA) to produce nearly locally optimal codes in a few minutes, and a code extender that uses exhaustive search

• Type: Conference
• Year: 2007
• Where: CIBCB
• Authors: Qinru Qiu, Daniel J. Burns, Qing Wu, Prakash Mukre
• Keywords: CIBCB 2007, Computational Biology, DNA Based Computing, DNA Codeword Library, Reliable Dna Codewords