Sequencing and Analysis of the Hydra Genome
Chapman, Kirkness et al., Nature
An international research collaboration reports their sequencing and analysis of the Hydra magnipapillata genome, and compare it to the genomes of several other organisms. "The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle," the authors write. They team suggests that comparisons of the Hydra genome to the reported sequences of other animals have helped them to elucidate the evolution of several of the organism's characteristics.
FPGAs Speedup Dot Plot
November 10, 2009
Buried beneath all the hype of Cloud Computing, multicore processing, and GPUs, FPGAs have not had much lip-service as of late, at least as far as life sciences applications go. But the folks over at Pico Computing have just announced a 5,000X speedup of a DNA sequence analysis and dot plot algorithm using an FPGA cluster consisting of 112 commodity cards. While not exactly evident in the press release, Mark Hur, director of sales & marketing kindly informed me that this is a 5,000x speedup over an Intelcore2Duo 2.66 GHz processor. The dot plot algorithm was written in C and ported to the FPGA using a C-to-FPGA tool provided by Impulse Accelerated Technologies. Here is a link to the white paper.
This is particularly
This is particularly impressive given that the port was done by a C-to-FPGA tool, not by an expensive hardware guy. The need for an FPGA guru is what has kept reconfigurable computing down for so long. How much does one of these Pico cards cost?