Cluster of re-configurable nodes for scanning large genomic banks

Genomic data are growing exponentially and are daily searched by thousands of biologists. To reduce the search time, efficient parallelism can be exploited by dispatching data among a cluster of processing units able to scan locally and independently their own data. If PC clusters are well suited to support this type of parallelism, we propose to substitute PCs by reconfigurable hardware closely connected to a hard disk. We show that low cost FPGA nodes interconnected through a standard Ethernet network may advantageously compete against high performance clusters. A prototype of 48 reconfigurable processing nodes has been experimented on content-based similarity and pattern search.