Dominique Lavenier and Mathieu Giraud, Chapter " Bioinformatics Applica- Tions " , in Reconfigurable Computing – Accelerating Computation with Field- Programmable Gate Arrays, Edited

Bioinformatics refers to the analysis and the management of biological information. The term computational biology is more often used to address physical and mathematical simulations of biological processes. The need for bioinformatics capabilities has been precipitated by the explosion of publicly available genomic information resulting from the Human Genome Project. The goal was to determine the sequence of the entire human genome (approximately three billion characters named base pairs, bp). The science of bioinformatics, which is the melding of molecular biology with computer science , is essential to the use of genomic information in understanding human diseases and in the identification of new molecular targets for drug discovery. Bioinformatics covers a large field of domains ranging from text sequence analysis to gene network modeling, 3D protein structure prediction, gene expression data analysis through DNA-chip, phylogeny, etc. But, for the last decade, the deluge of genomic information has led to an absolute requirement for computerized databases to store, organize, and index the data and for specialized tools to view and analyze genomic data. This is in this last domain – analysis of genomic data – that FPGA accelerators have exhibited extremely good performance for time consuming bioinformatics computations over a huge volume of data. They have demonstrated that they can be a viable alternative compared to supercomputers or clusters in both industrial [76, 78] and academic projects dedicated to intensive bio-computing algorithms : in 2003 and 2004, more than ten different teams published papers on FPGA implementations of sequence similarity search! Genomic data consist of DNA or protein sequences. A DNA sequence may be as simple as a single gene (a few thousands characters) or as complex as a complete genome (three billions characters for the human genome). DNA strings are sequences of nucleotides that range over the 4-letters alphabet Σ 4 = {A, C, G, T}. This alphabet leads to a compact 2-bit encoding scheme, well suited for FPGA hardware optimization compared to a 32-or 64-bit