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Related Concept Videos

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

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...
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

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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.
Phylogenetic Trees03:21

Phylogenetic Trees

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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,...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...

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Related Experiment Video

Updated: May 28, 2026

A Practical Guide to Phylogenetics for Nonexperts
12:00

A Practical Guide to Phylogenetics for Nonexperts

Published on: February 5, 2014

NAPP: the Nucleic Acid Phylogenetic Profile Database.

Alban Ott1, Anouar Idali, Antonin Marchais

  • 1Institut de Génétique et Microbiologie, UMR 8621, CNRS, Université Paris Sud, bâtiment 400, 91405 Orsay Cedex, France.

Nucleic Acids Research
|October 11, 2011
PubMed
Summary
This summary is machine-generated.

Nucleic acid phylogenetic profiling (NAPP) identifies functional non-coding RNAs by analyzing sequence conservation patterns across genomes. This improved method aids in discovering novel RNA genes without needing conserved secondary structures.

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
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Last Updated: May 28, 2026

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Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
08:57

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Published on: August 14, 2018

Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Identifying functional non-coding RNAs (ncRNAs) is crucial for understanding genome regulation.
  • Existing pipelines often rely on conserved RNA secondary structures, potentially missing novel ncRNA genes.
  • Nucleic acid phylogenetic profiling (NAPP) offers an alternative approach based on sequence conservation patterns.

Purpose of the Study:

  • To present an improved Nucleic acid phylogenetic profiling (NAPP) pipeline.
  • To identify and analyze functional non-coding elements, including small and cis-regulatory RNAs, in bacterial and archaeal genomes.
  • To provide a web interface and database for exploring NAPP-identified clusters.

Main Methods:

  • Applied an enhanced NAPP pipeline to a dataset of 949 bacterial and 68 archaeal genomes.
  • Classified coding and non-coding sequences based on cross-genome conservation profiles.
  • Developed a web interface for detailed analysis, visualization, and extraction of predicted RNAs.

Main Results:

  • The NAPP pipeline efficiently distinguishes clusters of functional non-coding elements.
  • NAPP identified conserved non-coding RNAs without requiring conserved secondary structures.
  • The analysis revealed clusters containing both coding and non-coding sequences with similar phylogenetic profiles, enabling functional analysis.

Conclusions:

  • The improved NAPP pipeline is effective for discovering novel RNA genes and functional non-coding elements.
  • NAPP complements existing methods by not relying on RNA secondary structure conservation.
  • The NAPP database and web interface facilitate further research into ncRNA function and evolution.