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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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Genomic Imprinting and Inheritance02:30

Genomic Imprinting and Inheritance

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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
The expression of some genes depends on which parent passed the gene to the offspring, through a phenomenon known as...
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Genome Size and the Evolution of New Genes03:21

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Genome Size and the Evolution of New Genes03:21

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Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

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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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Genomic DNA in Prokaryotes00:46

Genomic DNA in Prokaryotes

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The genome of most prokaryotic organisms consists of double-stranded DNA organized into one circular chromosome in a region of cytoplasm called the nucleoid. The chromosome is tightly wound, or supercoiled, for efficient storage. Prokaryotes also contain other circular pieces of DNA called plasmids. These plasmids are smaller than the chromosome and often carry genes that confer adaptive functions, such as antibiotic resistance.
Genomic Diversity in Bacteria
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Ultra-long Read Sequencing for Whole Genomic DNA Analysis
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Ultra-long Read Sequencing for Whole Genomic DNA Analysis

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PiGx: reproducible genomics analysis pipelines with GNU Guix.

Ricardo Wurmus1, Bora Uyar1, Brendan Osberg1

  • 1Bioinformatics Platform, The Berlin Institute for Medical Systems Biology, Max-Delbrück Center for Molecular Medicine, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.

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This study introduces GNU Guix for reproducible bioinformatics workflows, ensuring consistent results across different environments. The PiGx pipelines offer automated analysis for various sequencing types, simplifying data processing for researchers.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Scientific Computing

Background:

  • Reproducibility and traceability are critical in computationally intensive research fields like bioinformatics.
  • Managing software dependencies and versioning complexities hinders consistent workflow execution.
  • Rapidly evolving technologies exacerbate reproducibility challenges in bioinformatics.

Purpose of the Study:

  • To propose a principled approach for building reproducible analysis pipelines using GNU Guix.
  • To develop and present the PiGx suite of pipelines for various next-generation sequencing data analyses.
  • To enable users with minimal computational expertise to process their own datasets reproducibly.

Main Methods:

  • Utilizing GNU Guix for dependency management and environment control in bioinformatics workflows.
  • Developing the PiGx pipelines for RNA sequencing, ChIP sequencing, bisulfite sequencing, and single-cell RNA sequencing.
  • Automating the processing of raw experimental data into comprehensive reports with publication-ready figures.

Main Results:

  • Demonstrated highly reproducible analysis pipelines (PiGx) for multiple sequencing technologies.
  • Generated reports with interactive elements and standard observables from raw data.
  • Provided accessible installation and application of pipelines for users without advanced computational skills.

Conclusions:

  • GNU Guix offers a robust framework for achieving reproducible bioinformatics workflows.
  • The PiGx pipelines provide a practical solution for automated, reproducible analysis of diverse sequencing data.
  • This approach serves as a blueprint for enhancing reproducibility in computational research beyond bioinformatics.