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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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.
Next-Generation Sequencing Methods
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Long-patch Base Excision Repair01:02

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Since the discovery of the two BER pathways, there has been a debate about how a cell chooses one pathway over the other and the factors determining this selection. Numerous in vitro experiments have pointed out multiple determinants for the sub-pathway selection. These are:
Sanger Sequencing01:57

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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...
RNA-seq03:21

RNA-seq

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RACE - Rapid Amplification of cDNA Ends02:35

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Rapid Amplification of cDNA Ends, or RACE, is one of the most effective methods to obtain a full-length cDNA from an mRNA sequence between a known internal region to the unknown sequence at the 5’ or 3’ end. The unknown region is cloned in the cDNA by a gene-specific primer that binds the known end, and a hybrid primer that attaches a predefined anchor sequence to the unknown end of the cDNA. The sequence in between is amplified by PCR with an anchor primer and a gene-specific primer.
Since the...
Conservative Site-specific Recombination and Phase Variation02:53

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G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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LOCAS--a low coverage assembly tool for resequencing projects.

Juliane D Klein1, Stephan Ossowski, Korbinian Schneeberger

  • 1University of Tübingen, Tübingen, Germany. kleinj@informatik.uni-tuebingen.de

Plos One
|August 23, 2011
PubMed
Summary
This summary is machine-generated.

LOCAS is a novel assembler for low-coverage eukaryotic genome sequencing. It excels at homology-guided assembly, improving contig size and error rates for detecting sequence variations.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next Generation Sequencing (NGS) is crucial for detecting sequence variations in related genomes.
  • Low-coverage NGS data, like that from the Human 1000 Genomes Project, enables large-scale individual sequencing.
  • Current computational methods struggle to identify novel insertions or divergent sequences from low-coverage NGS data.

Purpose of the Study:

  • To develop a computational method for assembling low-coverage eukaryotic genomes.
  • To enable the discovery of novel sequence variations, including insertions and highly diverged regions, from low-coverage NGS data.

Main Methods:

  • Development of LOCAS, a novel NGS assembler utilizing a mismatch-sensitive overlap-layout-consensus approach.
  • LOCAS employs homology-guided assembly for homologous regions and de novo assembly for insertions and polymorphic regions.
  • Evaluation of LOCAS on low-coverage Arabidopsis thaliana strains from the Arabidopsis 1001 Genomes Project.

Main Results:

  • LOCAS demonstrates superior performance in homology-guided assembly of low-coverage eukaryotic genomes.
  • It achieves comparable assembly of long insertions to state-of-the-art assemblers.
  • LOCAS outperforms existing methods in contig size, error rate, and runtime.

Conclusions:

  • LOCAS is highly effective for homology-guided assembly of eukaryotic genomes using short reads and low sequencing depth.
  • It is a suitable tool for detecting novel sequence variations in low-coverage NGS datasets.
  • The assembler provides excellent results, making it a preferred choice for specific genomic assembly challenges.