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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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Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
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Genomic DNA in Prokaryotes00:46

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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.
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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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Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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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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Synthetic Biology02:55

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Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
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Updated: Dec 10, 2025

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
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Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale.

Edward E Seabolt, Gowri Nayar, Harsha Krishnareddy

    IEEE/ACM Transactions on Computational Biology and Bioinformatics
    |September 3, 2020
    PubMed
    Summary
    This summary is machine-generated.

    A new database, the Functional Genomics Platform, accelerates microbial genomic analysis by pre-computing relationships between biological entities. This tool provides faster insights into genotype-phenotype connections for bacterial life.

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    Area of Science:

    • Genomics
    • Bioinformatics
    • Microbial Ecology

    Background:

    • Biological sequence data is rapidly expanding, challenging traditional bioinformatics tools with computational demands.
    • Existing methods require significant time and large indices for analyzing vast genomic datasets.

    Purpose of the Study:

    • To develop a comprehensive database, the Functional Genomics Platform, for efficient genotype-to-phenotype analysis in bacteria.
    • To address computational challenges in analyzing large-scale microbial genomic data.

    Main Methods:

    • Pre-computation of relationships between biological entities within the Central Dogma of Molecular Biology.
    • Creation of a relational database storing curated genomic data, gene, protein, and domain information.
    • Development of developer tools including Python SDK and REST APIs for data access.

    Main Results:

    • The Functional Genomics Platform contains data from 200,000 genomes, 68 million genes, 52 million proteins, and 239 million domains.
    • The database enables querying hundreds of millions of entities with significantly reduced computation time.
    • Annotations from Gene Ontology, KEGG, MetaCyc, and Reactome are integrated, mapping complex biological connections.

    Conclusions:

    • The Functional Genomics Platform offers a scalable and efficient solution for microbial genomic research.
    • Researchers can gain faster insights into genotype-phenotype relationships for applications in infectious disease and environmental health.
    • The platform's architecture and developer tools facilitate large-scale studies of microbial life.