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Related Concept Videos

Phylogenetic Trees03:21

Phylogenetic Trees

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Phylogenetic trees come in many forms. It matters in which sequence the organisms are arranged from the bottom to the top of the tree, but the branches can rotate at their nodes without altering the information. The lines connecting individual nodes can be straight, angled, or even curved.
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Evolutionary Relationships through Genome Comparisons02:54

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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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Phylogeny is concerned with the evolutionary diversification of organisms or groups of organisms. A group of organisms with a name is called a taxon (singular). Taxa (plural) can span different levels of the evolutionary hierarchy. For instance, the group containing all birds is a taxon (comprising the class Aves), and the group of all species of daisies (the genus Bellis) is a taxon. Phylogenies can likewise include just one genus (i.e., depict species relationships) or span an entire kingdom.
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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Molecular taxonomy has revolutionized the understanding and classification of bacteria, providing precise insights into their diversity, evolutionary relationships, and ecological roles. By utilizing molecular techniques such as DNA sequencing and fingerprinting, researchers have made significant strides in various fields related to bacterial studies.Resolving Taxonomic AmbiguitiesMolecular taxonomy has been instrumental in distinguishing closely related bacterial species initially thought to...
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Single Nucleotide Polymorphisms-SNPs01:05

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Evidente-a visual analytics tool for data enrichment in SNP-based phylogenetic trees.

Mathias Witte Paz1, Theresa A Harbig1, Kay Nieselt1

  • 1Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72076, Germany.

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Summary

Evidente is a new web application that integrates phylogenetic trees with single-nucleotide polymorphism (SNP) data and metadata. This tool aids in linking genomic and phenotypic properties for pathogen strain analysis.

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Area of Science:

  • * Microbiology and Evolutionary Genomics
  • * Bioinformatics and Computational Biology

Background:

  • * Phylogenetic trees based on single-nucleotide polymorphisms (SNPs) are crucial for analyzing pathogen evolution.
  • * Integrating SNP data with metadata enhances the understanding of genomic and phenotypic links.

Purpose of the Study:

  • * To introduce Evidente, a web application for interactive visual analysis of phylogenetic trees, SNP data, and metadata.
  • * To facilitate the simultaneous interrogation of evolutionary relationships and sample characteristics.

Main Methods:

  • * Development of a web-application (Evidente) for interactive visualization.
  • * Classification of SNPs as supporting or non-supporting of phylogenetic tree structures.
  • * Integration of sample metadata and Gene Ontology (GO) term enrichment analysis.

Main Results:

  • * Evidente visualizes phylogenetic trees, SNP distributions, and associated metadata.
  • * The tool identifies SNPs supporting or contradicting tree topology.
  • * Enrichment analysis highlights over-represented genomic features within clades.

Conclusions:

  • * Evidente provides a comprehensive platform for exploring pathogen genomic data.
  • * The tool enhances the interpretation of evolutionary history by linking genomic and phenotypic data.
  • * Usability demonstrated with *Treponema pallidum* and *Mycobacterium leprae* data.