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Related Concept Videos

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Genomics02:02

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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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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: Aug 27, 2025

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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GBZ file format for pangenome graphs.

Jouni Sirén1, Benedict Paten1

  • 1Genomics Institute, University of California, Santa Cruz, CA 95064, USA.

Bioinformatics (Oxford, England)
|September 30, 2022
PubMed
Summary

A new file format, GBZ, efficiently stores repetitive pangenome graph data. This format offers good compression and fast loading for genome assembly analysis.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Pangenome graphs are crucial for representing multiple genome assemblies.
  • Current file formats struggle with the storage of repetitive data in growing pangenome datasets.

Purpose of the Study:

  • To introduce a novel, efficient file format for pangenome graphs.
  • To address the limitations of existing formats in handling repetitive genomic data.

Main Methods:

  • Developed the GBZ (Genome graph) file format.
  • Utilized data structures from the Giraffe short-read aligner.
  • Created compression and decompression tools and libraries for GBZ graphs.

Main Results:

  • The GBZ format achieves good compression ratios for pangenome graph data.

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  • GBZ files can be efficiently loaded into in-memory data structures.
  • Demonstrated efficient usability of GBZ graphs across various systems.

    • Conclusions:

    • The GBZ file format provides an efficient solution for storing and managing large pangenome graph data.
    • GBZ facilitates scalable pangenome analysis by improving data storage and accessibility.