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Related Concept Videos

Phylogeny01:23

Phylogeny

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.
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

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...
Phylogenetic Trees03:21

Phylogenetic Trees

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.
Phylogenetic Trees03:21

Phylogenetic Trees

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.
Microbial Phylogeny01:28

Microbial Phylogeny

Understanding the evolutionary relationships among microorganisms is fundamental to microbial ecology and taxonomy. Phylogenetic trees are essential tools for inferring these relationships, relying primarily on comparative analyses of molecular sequences such as DNA, RNA, or proteins. In microbial studies, these trees typically depict the evolutionary paths of diverse bacterial and archaeal species by mapping genetic differences accumulated over time.Phylogenetic trees are composed of tips,...
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes02:16

Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes

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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De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data
08:23

De novo Identification of Actively Translated Open Reading Frames with Ribosome Profiling Data

Published on: February 18, 2022

Open reading frame phylogenetic analysis on the cloud.

Che-Lun Hung1, Chun-Yuan Lin

  • 1Department of Computer Science and Communication Engineering, Providence University, Taichung 43301, Taiwan.

International Journal of Genomics
|May 15, 2013
PubMed
Summary
This summary is machine-generated.

This study introduces a cloud-based service for analyzing viral evolutionary relationships using open reading frames. The platform accurately identifies relationships, as demonstrated by a Norovirus case study.

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Area of Science:

  • Bioinformatics
  • Virology
  • Computational Biology

Background:

  • Phylogenetic analysis is crucial for understanding viral evolution and is typically based on sequence similarity.
  • Viral evolutionary relationships are determined from open reading frames (ORFs), not complete genomes.
  • Cloud computing offers scalable solutions for developing bioinformatics tools.

Purpose of the Study:

  • To propose and evaluate a novel cloud-based service for phylogenetic analysis of viral open reading frames.
  • To leverage cloud infrastructure for efficient and large-scale bioinformatics services.

Main Methods:

  • Development of a cloud-based service integrating the Hadoop framework and virtualization technology.
  • Implementation of phylogenetic analysis methods for open reading frame sequences.
  • Case study involving phylogenetic analysis of Norovirus sequences.

Main Results:

  • The proposed service provides a high-availability and scalable platform for bioscience.
  • The cloud-based approach correctly elucidates evolutionary relationships among Norovirus strains.
  • Accurate identification of evolutionary pathways through ORF sequence alignment.

Conclusions:

  • The developed cloud-based open reading frame phylogenetic analysis service is effective and scalable.
  • This approach enhances the study of viral evolutionary relationships, particularly for viruses like Norovirus.
  • Cloud computing provides a robust framework for advanced bioinformatics research.