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Related Concept Videos

Next-generation Sequencing03:00

Next-generation Sequencing

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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.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....
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Sanger Sequencing01:57

Sanger Sequencing

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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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FISH - Fluorescent In-situ Hybridization02:07

FISH - Fluorescent In-situ Hybridization

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Fluorescence in situ hybridization, or FISH, was developed in the early 1980s and has quickly become one of the most widely used techniques in cytogenetics. Labeled probes are used to bind complementary DNA or RNA sequences on a chromosome or in a region within a cell. Earlier, the probes could only be obtained by cloning or reverse transcription of a DNA template. Currently, the probe oligonucleotides can be synthesized synthetically. Additionally, with the advancement of optical techniques,...
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Signal Flow Graphs01:18

Signal Flow Graphs

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Signal-flow graphs offer a streamlined and intuitive approach to representing control systems, providing an alternative to traditional block diagrams. These graphs use branches to symbolize systems and nodes to represent signals, effectively illustrating the relationships and interactions within the system.
In a signal-flow graph, branches denote the system's transfer functions, while nodes represent the signals. The direction of signal flow is indicated by arrows, with the corresponding...
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Signal Sequences and Sorting Receptors01:41

Signal Sequences and Sorting Receptors

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Signal sequences are short amino acid sequences that guide newly synthesized proteins to their proper location within the cell. Classical signal sequences are fifteen to sixty amino acids long and present at the N-terminus of a polypeptide chain. Each signal sequence has a conserved segment of basic residues towards their N terminus, a hydrophobic core, and a C-terminus rich in polar residues. The C-terminus also contains a signal cleavage site and features a -3 -1 sequence motif. The -3-1...
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RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Related Experiment Video

Updated: Nov 22, 2025

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq
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recoup: flexible and versatile signal visualization from next generation sequencing.

Panagiotis Moulos1

  • 1Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center 'Alexander Fleming', Fleming 34, 16672, Vari, Greece. moulos@fleming.gr.

BMC Bioinformatics
|January 7, 2021
PubMed
Summary

The recoup Bioconductor package offers fast, user-friendly visualization of genomic sequencing data. It provides publication-quality plots with enhanced reusability and reproducibility for biological research.

Keywords:
ATAC-SeqChIP-SeqGenomic profilesNext generation sequencingRNA-SeqSignal visualizationTranscription factors

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Increasingly large genomic datasets from new sequencing protocols necessitate efficient data summarization and visualization.
  • Existing tools often lack user-friendliness, reproducibility, or comprehensive visualization capabilities for genomic signal analysis.

Purpose of the Study:

  • To develop a novel software package for quick, comprehensive, and repeatable visualization of genomic signal data.
  • To address the need for user-friendly tools that can handle large-scale genomic datasets.

Main Methods:

  • Development of the recoup Bioconductor package.
  • Integration with a database of precalculated genomic regions for multiple organisms.
  • Implementation of processing mechanisms for efficient data interrogation and visualization.

Main Results:

  • recoup provides quick, flexible, and accurate visualization of genomic coverage profiles from Next Generation Sequencing (NGS) data.
  • The package facilitates multi-level data interrogation and generates publication-quality visualizations.
  • recoup excels in plot reusability, reproducibility, and real-time exploration, balancing speed, quality, and user-friendliness.

Conclusions:

  • recoup offers a balanced solution for genomic data visualization, overcoming limitations of existing tools in terms of user-friendliness and reproducibility.
  • The package is fast, friendly, and provides a unique tradeoff of key features for effective genomic data analysis.