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Related Concept Videos

Structural Information from Single-molecule FRET Experiments Using the Fast Nano-positioning System12:30

Structural Information from Single-molecule FRET Experiments Using the Fast Nano-positioning System

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We present the setup and experimental procedure to obtain smFRET data from large donor-acceptor networks with a TIRF microscope. The step-by-step analysis of these measurements with the Bayesian inference software Fast-NPS yields high-resolved structural information via the application of adapted dye...
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Method for Labeling Transcripts in Individual Escherichia coli Cells for Single-molecule Fluorescence In Situ Hybridization Experiments07:51

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This manuscript describes a method for labeling individual messenger RNA (mRNA) transcripts with fluorescently-labeled DNA probes, for use in single-molecule fluorescence in situ hybridization (smFISH) experiments in E. coli. smFISH is a visualization method that allows the simultaneous detection, localization, and quantification of single mRNA molecules in fixed individual...
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Human behavior is intricately shaped by social influences that arise from interactions with others in diverse contexts. These influences not only mold beliefs and attitudes but also drive the regulation of behaviors through both direct communication and observational learning. The study of these processes falls within the domain of social psychology, which seeks to understand how individuals are affected by and affect those around them.Mechanisms of Social InfluenceDirect social influence...
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A method for microdissection of the mouse oviduct that allows collection of the individual segments while maintaining RNA integrity is presented. In addition, non-enzymatic oviductal cell dissociation procedure is described. The methods are appropriate for subsequent gene and protein analysis of the functionally different oviductal segments and dissociated oviductal...
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Related Experiment Video

Updated: Jan 19, 2026

Structural Information from Single-molecule FRET Experiments Using the Fast Nano-positioning System
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Fast single individual haplotyping method using GPGPU.

Joong Chae Na1, Inbok Lee2, Je-Keun Rhee3

  • 1Department of Computer Science and Engineering, Sejong University, Seoul, 05006, South Korea.

Computers in Biology and Medicine
|September 10, 2019
PubMed
Summary
This summary is machine-generated.

Graphic Processing Units (GPUs) significantly accelerate next-generation sequencing (NGS) data analysis. Parallelizing the Probabilistic Evolutionary Algorithm with Toggling for Haplotyping (PEATH) method on GPUs (PEATH/G) dramatically reduces computation time for faster haplotyping.

Keywords:
CUDAGPGPUNext generation sequencingPEATH/GSingle individual haplotyping

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Related Experiment Videos

Last Updated: Jan 19, 2026

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Next-generation sequencing (NGS) data analysis demands substantial computational resources.
  • Existing bioinformatic tools often require significant processing power.

Purpose of the Study:

  • To assess the utility of graphic processing units (GPUs) for accelerating NGS data computation.
  • To evaluate the performance of a parallelized haplotyping algorithm on GPUs.

Main Methods:

  • Parallelization of the Probabilistic Evolutionary Algorithm with Toggling for Haplotyping (PEATH) method using general-purpose computing on GPU (GPGPU), creating PEATH/G.
  • Testing PEATH/G on NA12878 fosmid-sequencing and HuRef datasets using NVIDIA GeForce GTX 1660Ti and GTX 950 GPUs.

Main Results:

  • PEATH/G demonstrated significant speedups, running 46.8x and 25.4x faster than PEATH on the tested datasets.
  • Even an inexpensive GPU (GTX 950) provided a 13.3x speed increase for fosmid-sequencing data.
  • The parallelized tool maintained accuracy while enhancing computational efficiency.

Conclusions:

  • PEATH/G offers a practical solution for single-individual haplotyping, balancing accuracy and speed.
  • General-purpose computing on GPU (GPGPU) effectively reduces the computational time for NGS analysis tools.