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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,...
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.
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.
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...

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A Practical Guide to Phylogenetics for Nonexperts
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Published on: February 5, 2014

The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree

Cyrus Afrasiabi1, Bushra Samad, David Dineen

  • 1QB3 Institute, University of California, Berkeley, Berkeley, CA 94720-1762, USA.

Nucleic Acids Research
|May 21, 2013
PubMed
Summary
This summary is machine-generated.

The Fast Approximate Tree Classification (FAT-CAT) web server accurately identifies protein orthologs using hidden Markov models. This tool aids in predicting gene function across diverse species with high precision.

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An Integrated Approach for Microprotein Identification and Sequence Analysis
09:37

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Published on: July 12, 2022

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Phylogenetics

Background:

  • Ortholog identification is crucial for understanding gene function and evolutionary relationships.
  • Existing methods face challenges with paralogs and proteins containing promiscuous domains.
  • PhyloFacts database offers extensive protein data for phylogenetic analysis.

Purpose of the Study:

  • To introduce the Fast Approximate Tree Classification (FAT-CAT) web server for ortholog identification.
  • To evaluate FAT-CAT's precision and robustness in classifying orthologs and paralogs.
  • To enable functional annotation of protein sequences using phylogenetic placement.

Main Methods:

  • Utilizing subtree hidden Markov models (HMMs) for protein sequence placement.
  • Integrating HMM scoring for precise ortholog identification.
  • Leveraging the PhyloFacts database (>7.3 million proteins) for comprehensive analysis.

Main Results:

  • FAT-CAT demonstrates high precision in distinguishing orthologs from paralogs across microbial, plant, and animal proteins.
  • The method shows robustness against promiscuous protein domains.
  • Functional annotations with confidence scores are derived from phylogenetic placement.

Conclusions:

  • FAT-CAT provides a powerful and accurate approach for ortholog identification and functional annotation.
  • The PhyloFacts database and FAT-CAT web server offer broad taxonomic and functional coverage.
  • Adjustable parameters and interactive visualization tools enhance user accessibility and utility.