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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
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DNA sequencing is a fundamental technique that is routinely used in the biological sciences. This method can be applied to a range of questions at different scales - from the sequencing of a cloned DNA fragment or the study of a mutation in a gene up to whole-genome sequencing. However, despite the widespread use of sequencing today, it was not until 1977 that Fredrick Sanger and his collaborators developed the chain-termination method to decode DNA sequences. It relies on the separation of a...
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Eukaryotes have large genomes compared to prokaryotes. To fit their genomes into a cell, eukaryotic DNA is packaged extraordinarily tightly inside the nucleus. To achieve this, DNA is tightly wound around proteins called histones, which are packaged into nucleosomes that are joined by linker DNA and coil into chromatin fibers. Additional fibrous proteins further compact the chromatin, which is recognizable as chromosomes during certain phases of cell division.
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Related Experiment Video

Updated: Mar 13, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing

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VSEARCH: a versatile open source tool for metagenomics.

Torbjørn Rognes1, Tomáš Flouri2, Ben Nichols3

  • 1Department of Informatics, University of Oslo, Oslo, Norway; Department of Microbiology, Oslo University Hospital, Oslo, Norway.

Peerj
|October 27, 2016
PubMed
Summary
This summary is machine-generated.

VSEARCH is a free, open-source tool for sequence analysis, offering an accurate and versatile alternative to USEARCH for metagenomics and genomics data processing. It provides enhanced functionality and improved accuracy in various analyses.

Keywords:
AlignmentChimera detectionClusteringDereplicationMaskingMetagenomicsParallellizationSearchingSequencesShuffling

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • VSEARCH is a free, open-source, multithreaded tool for processing nucleotide sequence data in metagenomics, genomics, and population genomics.
  • It serves as an alternative to the proprietary USEARCH tool, addressing limitations in accessibility and algorithmic transparency.

Purpose of the Study:

  • To introduce VSEARCH as a comprehensive and freely available alternative for sequence data analysis.
  • To highlight its capabilities, performance, and advantages over existing tools like USEARCH.

Main Methods:

  • VSEARCH employs a fast heuristic for initial sequence searching, followed by optimal global sequence alignment using full dynamic programming.
  • Pairwise alignments are parallelized using vectorization and multiple threads for efficient computation.

Main Results:

  • VSEARCH replicates most USEARCH commands and adds new functionalities, including advanced chimera detection, sequence masking, and FASTQ processing.
  • It demonstrates higher accuracy than USEARCH in searching, clustering, chimera detection, and subsampling, with competitive or superior speed in specific tasks like dereplication and read merging.

Conclusions:

  • VSEARCH is a fast, accurate, and feature-rich open-source tool for sequence analysis.
  • It provides the scientific community, particularly in metagenomics, with a versatile and accessible alternative to proprietary software.