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Related Concept Videos

Strategies of Self-Presentation I: Strategic Self-Presentation01:12

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Strategic self-presentation refers to individuals' intentional efforts to influence how others perceive them. This process is employed in various social and professional settings, such as job interviews, dating, politics, and legal contexts, where individuals seek to shape impressions to gain social or material advantages. While people generally present themselves in ways that align with their authentic characteristics, external factors, such as cognitive load, can hinder their ability to...
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Protein glycosylation starts in the ER lumen and continues in the Golgi apparatus. Glycosyltransferases catalyze the addition of sugar molecules or glycosylation of proteins. Usually, these enzymes add sugars to the hydroxyl groups of selected serine or threonine residues to form O-linked glycans or the amino groups of asparagine residues to form N-linked glycans. Different positions on the same polypeptide chain can contain differently linked glycans.
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Cytoskeletal filaments are polymeric forms of smaller protein subunits. However, individual cytoskeletal filaments may easily disassemble or associate with other similar filaments to form rigid structures. Microfilaments, made of actin monomers, rely on actin-binding proteins to form bundles and create networks of individual actin filaments. Microtubules rely on microtubule-associated proteins (MAPs) to form sturdy cylindrical structures. However, the proteins involved in forming complex...
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SKESA: strategic k-mer extension for scrupulous assemblies.

Alexandre Souvorov1, Richa Agarwala2, David J Lipman1,3

  • 1NCBI/NLM/NIH/DHHS, 8600 Rockville Pike, Bethesda, 20894, MD, USA.

Genome Biology
|October 6, 2018
PubMed
Summary

SKESA is a fast de novo assembler for microbial genomes, producing high-quality, contiguous assemblies. It reliably handles contamination and ensures reproducible results, making it ideal for large-scale genomic projects.

Keywords:
ContaminationDe-novo assemblyDeBruijn graphsIllumina readsSequence quality

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • De novo genome assembly is crucial for understanding microbial genomes.
  • Existing assemblers face challenges with read quality, contamination, and reproducibility.
  • Efficient assembly tools are needed for large-scale sequencing projects.

Purpose of the Study:

  • To introduce SKESA, a novel DeBruijn graph-based assembler for microbial genomes.
  • To evaluate SKESA's performance against established assemblers like SPAdes and MegaHit.
  • To highlight SKESA's capabilities in handling contamination and ensuring assembly consistency.

Main Methods:

  • SKESA utilizes a DeBruijn graph approach for sequence assembly.
  • Comparative analysis was performed using Illumina sequencing reads from microbial genomes.
  • Performance metrics included assembly quality, contiguity, speed, and reproducibility.

Main Results:

  • SKESA demonstrates superior or comparable sequence quality and contiguity to SPAdes and MegaHit.
  • The assembler effectively manages low-level contamination present in sequencing reads.
  • SKESA provides identical assembly outputs across multiple runs, irrespective of computational resources.

Conclusions:

  • SKESA is a robust and efficient tool for de novo assembly of microbial genomes.
  • Its speed, accuracy, and reproducibility make it suitable for large-scale applications, including pathogen detection.
  • SKESA is publicly available, promoting its adoption in the research community.