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Related Concept Videos

Directing Effect of Substituents: meta-Directing Groups01:09

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Substituents on the benzene ring that direct an incoming electrophile to undergo substitution at the meta position are called meta directors. All meta directors either have a positive charge on the atom directly bonded to the ring or a partial positive charge. These groups function by withdrawing electrons from the ring through inductive and resonance effects. Consider the carbocation intermediates formed upon the addition of an electrophile on nitrobenzene at the...
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The alignment of a road line using Geographic Information Systems (GIS) is a critical process in civil engineering, combining advanced technology with practical decision-making. This methodology begins with the collection of geospatial data, including information on land cover, geomorphology, drainage patterns, slope, and contour details. Such data is typically acquired through satellite imagery and GIS tools, offering a comprehensive understanding of the terrain.Once the data is gathered, it...
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Aligning actions are communicative strategies individuals employ to maintain social harmony and preserve personal identity in the face of potential disruptions to social norms. These actions are particularly important in managing social impressions when one's behavior might be seen as inappropriate, incompetent, or morally questionable.Types of Aligning ActionsThe three principal types of aligning actions are disclaimers, accounts, and apologies.DisclaimersDisclaimers are preventive; they are...
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meta-Directing Deactivators: –NO2, –CN, –CHO, –⁠CO2R, –COR, –CO2H01:13

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All meta-directing substituents are deactivating groups. These substituents withdraw electrons from the aromatic ring, making the ring less reactive toward electrophilic substitution. For example, the nitration of nitrobenzene is 100,000 times slower than that of benzene because of the deactivating effect of the nitro group. The first step in an electrophilic aromatic substitution is the addition of an electrophile to form a resonance-stabilized carbocation. The energy diagrams for...
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Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
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IMOS: improved Meta-aligner and Minimap2 On Spark.

Mostafa Hadadian Nejad Yousefi1, Maziar Goudarzi2, Seyed Abolfazl Motahari1

  • 1Department of Computer Engineering, Sharif University of Technology, Azadi, Tehran, Iran.

BMC Bioinformatics
|January 26, 2019
PubMed
Summary
This summary is machine-generated.

IMOS is a novel aligner for mapping noisy long reads to reference genomes. This tool enhances accuracy and speed on single or distributed nodes, significantly reducing genome sequencing processing times.

Keywords:
AlignerBig dataDistributed processingLong readPacBio

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Area of Science:

  • Genomics
  • Bioinformatics

Background:

  • Long reads offer crucial genomic sequence data but are often noisy, complicating genome alignment.
  • Aligning noisy long reads on a single node can be time-consuming, taking days for human genome datasets.
  • High-performance, scalable aligners are essential for efficient distributed genome analysis.

Purpose of the Study:

  • To present IMOS, an aligner designed for mapping noisy long reads to reference genomes.
  • To offer a solution that operates efficiently on both single and distributed computing nodes.
  • To improve upon existing alignment tools in terms of speed and accuracy for long-read sequencing data.

Main Methods:

  • Developed IMOS as an improved version of Meta-aligner (IM) for single-node performance.
  • Implemented IMOS to run IM and Minimap2 on Apache Spark for distributed cluster deployment.
  • Evaluated multi-node IMOS performance against SparkBWA for long-read alignment tasks.

Main Results:

  • Single-node IMOS (IM) demonstrated up to a 6x speed increase over the original Meta-aligner.
  • Multi-node IMOS achieved significant speedups: 1.5x for IM and 25x for Minimap2 compared to SparkBWA.
  • IMOS architecture allows for near-linear speed increases with the addition of nodes in a cluster.

Conclusions:

  • IMOS provides an effective architecture for mapping noisy long reads to reference genomes.
  • The aligner's performance scales efficiently across distributed computing clusters.
  • IMOS is a versatile, multi-platform application compatible with Linux, Windows, and macOS.