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Related Concept Videos

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...
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,...
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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...
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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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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.The length of the branches can depict time or the relative amount of change among organisms. For instance, the branch length might indicate the number of amino acid changes in the sequence that underlies the...
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Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
08:03

Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations

Published on: December 7, 2021

SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny.

Derek Wilson1, Ralph Pethica, Yiduo Zhou

  • 1MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, Department of Computer Science, University of Bristol, The Merchant Venturers Building, Bristol BS8 1UB, UK. dw@mrc-1mb.cam.ac.uk

Nucleic Acids Research
|November 28, 2008
PubMed
Summary
This summary is machine-generated.

SUPERFAMILY is a protein database offering structural and evolutionary insights for over 900 genomes. It uses Hidden Markov Models for protein domain annotation, aiding evolutionary and functional studies.

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Area of Science:

  • Bioinformatics
  • Structural Biology
  • Genomics

Background:

  • Protein domain assignment is crucial for understanding protein function and evolution.
  • Databases like SUPERFAMILY integrate structural, functional, and evolutionary information.
  • Accurate domain annotation across diverse proteomes is essential for large-scale biological studies.

Purpose of the Study:

  • To provide comprehensive structural, functional, and evolutionary information for proteins.
  • To offer protein domain assignments for over 900 sequenced genomes.
  • To facilitate protein analysis through a user-friendly web interface and downloadable resources.

Main Methods:

  • Utilizes Hidden Markov Models (HMMs) based on Structural Classification of Proteins (SCOP) domain definitions.
  • Employs a new model library based on SCOP 1.73 for enhanced structural annotation.
  • Integrates data from completely sequenced genomes and large sequence collections like UniProt.

Main Results:

  • Provides protein domain assignments at both superfamily and family levels for over 900 genomes.
  • Enables users to submit sequences for SCOP domain classification.
  • Offers tools for searching, comparing domain architectures, and building multiple sequence alignments.

Conclusions:

  • SUPERFAMILY serves as a valuable resource for structural, functional, and evolutionary protein analysis.
  • Recent extensions enhance its utility with InterPro abstracts, Gene Ontology terms, and taxonomic visualization.
  • The database, models, and scripts are publicly accessible for download, promoting research accessibility.