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Related Concept Videos

Genomics02:02

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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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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An Educational Bioinformatics Project to Improve Genome Annotation.

Zoie Amatore1, Susan Gunn2, Laura K Harris1

  • 1Science Department, Harris Interdisciplinary Research, Davenport University, Lansing, MI, United States.

Frontiers in Microbiology
|December 28, 2020
PubMed
Summary

Students can now help improve genome annotation by analyzing hypothetical proteins (HPs) using bioinformatics tools. This project enhances understanding of protein functions and aids scientific advancement.

Keywords:
bioinformaticsclassroomeducationgenome annotationhypothetical proteinundergraduate

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Genome annotation is crucial for understanding protein function, but hypothetical proteins (HPs) with unknown functions hinder scientific progress.
  • Manual review is often necessary to verify and update genome annotations, a task that can be effectively undertaken by students.

Purpose of the Study:

  • To introduce an innovative classroom project, the Hypothetical Protein Characterization Project, for students to analyze HPs.
  • To determine if HPs have outdated or indeterminate annotations using bioinformatics resources.
  • To provide a customizable educational tool for learning bioinformatics and addressing scientific questions.

Main Methods:

  • Utilizing freely available, web-based bioinformatics resources to analyze amino acid sequences of HPs.
  • Analyzing sequence similarities, protein domains, tertiary structure, active sites, binding ligands, and cellular location.
  • Employing various HP selection strategies, including random selection, differential gene expression, and phylogenetic relations.

Main Results:

  • The project generates sufficient evidence to support re-annotation of HPs or prioritize them for experimental validation.
  • Students gain practical experience applying bioinformatics tools to real scientific problems.
  • The project is adaptable for diverse educational settings, including online and in-person instruction.

Conclusions:

  • The Hypothetical Protein Characterization Project offers a valuable pedagogical approach to improve genome annotation and advance biological understanding.
  • It empowers students to contribute to scientific research while developing critical bioinformatics skills.
  • This project enhances scientific literacy and research capabilities among students.