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Module 8: Genome annotation

2024-01-27

Overview

Module 8 is dedicated to the essential task of genome annotation in bacterial genomics. This process involves identifying and marking the various features within a genome, such as genes, coding sequences, regulatory elements, and other functional regions. Genome annotation is crucial for understanding the biological roles of these features and for further comparative genomic studies. The module will explore the methodologies and tools used for genome annotation, the interpretation of annotation data, and the challenges faced in accurately annotating complex bacterial genomes. Through practical labs, students will gain hands-on experience in annotating bacterial genomes and analyzing the results.

Introduction

  • The concept and importance of genome annotation in bacterial genomics
  • Overview of the types of genomic features that are annotated
  • The role of computational tools and databases in genome annotation

Topics

Fundamentals of Genome Annotation

  • The process of identifying genes and predicting their functions
  • Differentiating between coding and non-coding DNA
  • The use of sequence homology and orthology in functional annotation

Tools and Databases for Genome Annotation

  • Introduction to common annotation platforms (Prokaryotic Genome Annotation Pipeline (PGAP), RAST, Prokka)
  • Utilizing databases like NCBI, UniProt, and KEGG for annotation
  • Evaluating the strengths and limitations of different annotation approaches

Functional and Structural Annotation

  • Predicting gene functions based on sequence similarity and domain architecture
  • Identifying RNA genes, regulatory sequences, and operons
  • Understanding the role of manual curation in refining annotations

Challenges in Genome Annotation

  • Dealing with pseudogenes, paralogs, and horizontal gene transfer
  • Addressing incomplete or low-quality genome assemblies
  • The importance of updating annotations with new data and insights

#Labs

  • Lab 1: Automated Genome Annotation using RAST/Prokka
  • Lab 2: Functional Annotation and Database Searches
  • Lab 3: Manual Curation and Refinement of Genome Annotations

Learning Outcomes

By the end of this module, students will be able to:

  • Define genome annotation and its significance in the context of bacterial genomics.
  • Identify and describe the various genomic features that are annotated in bacterial genomes.
  • Utilize computational tools and databases to perform genome annotation.
  • Interpret and evaluate the results of genome annotation.
  • Understand the challenges in genome annotation and apply strategies to address them.
  • Perform manual curation to refine and validate genome annotations.
  • Communicate the results of genome annotation effectively in written and oral formats.