HELIOS: High-speed sequence alignment in optics
Table 20
Processing time of the HELIOS optical architecture, compared to Smith-waterman, assuming the SWISS-PROT database [64].
In this manner, various lengths of query sequences, from 144 to 5478 bases are aligned to the SWISS-PROT database [64], which contains 392,768 sequences and a total of 141,218,456 characters. In this regard, the processing times of Smith-waterman are reported by executing on NVIDIA TESLA K40 GPU with 44.3 giga cell updates per second (GCUPS) and GTX 275 with 21 GCUPS [65]. On the other hand, the processing times of HELIOS optical architecture are reported for a modulator with 1024 × 1024 pixels aperture size and 100 MHz switching rate [66] as a default, as well as for more recently developed modulators with various aperture sizes, such as 1920 × 1080 and 4096 × 4096 pixels, as well as various switching rates, including 35 GHz [72] and 4.5 THz [67].