RESUMEN

DNA sequencing is the physical/biochemical process of identifying the location of the four bases (Adenine, Guanine, Cytosine, Thymine) in a DNA strand. As semiconductor technology revolutionized computing, modern DNA sequencing technology (termed Next Generation Sequencing, NGS) revolutionized genomic research. As a result, modern NGS platforms can sequence hundreds of millions of short DNA fragments in parallel. The sequenced DNA fragments, representing the output of NGS platforms, are termed reads. Besides genomic variations, NGS imperfections induce noise in reads. Mapping each read to (the most similar portion of) a reference genome of the same species, i.e., read mapping, is a common critical first step in a diverse set of emerging bioinformatics applications. Mapping represents a search-heavy memory-intensive similarity matching problem, therefore, can greatly benefit from near-memory processing. Intuition suggests using fast associative search enabled by Ternary Content Addressable Memory (TCAM) by construction. However, the excessive energy consumption and lack of support for similarity matching (under NGS and genomic variation induced noise) renders direct application of TCAM infeasible, irrespective of volatility, where only non-volatile TCAM can accommodate the large memory footprint in an area-efficient way. This paper introduces GeNVoM, a scalable, energy-efficient and high-throughput solution. Instead of optimizing an algorithm developed for general-purpose computers or GPUs, GeNVoM rethinks the algorithm and non-volatile TCAM-based accelerator design together from the ground up. Thereby GeNVoM can improve the throughput by up to 3.67×; the energy consumption, by up to 1.36×, when compared to an ASIC baseline, which represents one of the highest-throughput implementations known.

Asunto(s)

Algoritmos , Programas Informáticos , Genómica , Computadores , Análisis de Secuencia de ADN , Secuenciación de Nucleótidos de Alto Rendimiento , ADN/genética

RESUMEN

Confocal fluorescence microscopy is a proven technique, which can image near-electrode pH changes. For a complete understanding of electrode processes, time-resolved measurements are required, which have not been achieved previously. Here we present the first measurements of time-resolved pH profiles with confocal fluorescence microscopy. The experimental results compare favorably with a one-dimensional reaction-diffusion model; this holds up to the point where the measurements reveal three-dimensionality in the pH distribution. Specific factors affecting the pH measurement such as attenuation of light and the role of dye migration are also discussed in detail. The method is further applied to reveal the buffer effects observed in sulfate-containing electrolytes. The work presented here is paving the way toward the use of confocal fluorescence microscopy in the measurement of 3D time-resolved pH changes in numerous electrochemical settings, for example, in the vicinity of bubbles.