Bacterial Bioinformatics

Go to Course: https://www.coursera.org/learn/informatics

Introduction

### Course Review: Bacterial Bioinformatics on Coursera #### Overview If you're looking to deepen your understanding of bacterial genomics and bioinformatics, the **Bacterial Bioinformatics** course on **Coursera** emerges as a highly recommended choice. This well-structured program provides comprehensive demonstrations and hands-on exercises for analyzing bacterial sequence data, all facilitated through the impressive **Bacterial and Viral Bioinformatics Resource Center (BV-BRC)**, an initiative funded by the NIH/NIAID. BV-BRC is a powerhouse of bacterial genomic data with integrated analysis tools and visualizations, making it ideal for both beginners and those with intermediate knowledge in bioinformatics. #### Course Breakdown The syllabus covers a wide array of essential topics, ensuring a thorough grounding in bacterial bioinformatics. Here's a brief overview of what you can expect in each module: 1. **Introduction** - The course begins with an introduction to BV-BRC, elaborating on its functionalities and the resources it offers. This is an excellent foundation for learners who may be new to bacterial research, as it highlights how to navigate the platform effectively. 2. **Assembly** - Participants will receive step-by-step guidance on assembling a genome from bacterial sequence reads. This hands-on component is particularly beneficial for those aiming to improve their technical skills in genome assembly. 3. **Annotation** - Following assembly, the course delves into genome annotation. Learners will engage in practical exercises to understand how to annotate a genome from contigs, further solidifying their grasp on the subject matter. 4. **Comprehensive Genome Analysis** - This module ties everything together by teaching users how to assemble, annotate, and conduct an automated analysis of a genome. The integration of these tasks is crucial for performing comprehensive genomic analyses. 5. **Codon-Based Phylogenetic Trees** - Here, learners explore how to generate phylogenetic trees from codon data, an essential skill for understanding evolutionary relationships among bacteria. 6. **Similar Genome Finder** - This segment instructs students on utilizing the Similar Genome Finder Service to locate analogous genomes within BV-BRC, enhancing comparative analysis capabilities. 7. **Protein Family Sorter** - Learners will gain proficiency in using the Protein Family Sorter, enabling them to compare protein presence and absence across different genomes—a valuable skill for anyone studying microbial ecology or evolution. 8. **Proteome Comparison** - The final lesson revolves around comparing an entire set of genomes against a reference genome, providing insights into genetic structure and function. Each of these modules is laid out with clear objectives and includes exercises to bolster comprehension. Importantly, although the course was developed using the earlier PATRIC platform, the content is still highly relevant and applicable through BV-BRC, ensuring learners are still equipped with pertinent skills. #### Recommendations **Who Should Enroll:** - Anyone interested in bacterial genomics, from students to seasoned researchers. - Bioinformatics professionals looking to refresh their skills or learn about a new platform. - Life scientists interested in understanding more about genomics and its applications in microbial research. **Why Take This Course:** - Comprehensive curriculum covering all key aspects of bacterial bioinformatics. - Hands-on exercises using a widely recognized bioinformatics platform (BV-BRC). - The course serves as a strong steppingstone for those looking to apply bioinformatics in real-world research scenarios, particularly in microbiology and infectious diseases. If you are passionate about bacterial genomics and want to equip yourself with the necessary analytical tools, the **Bacterial Bioinformatics** course on Coursera is an outstanding resource. The combination of its in-depth content, practical application, and reputable platform makes it a must-take for aspiring bioinformaticians!

Syllabus

Introduction

This lesson provides an introduction to BV-BRC, the Bacterial and Viral Resource Integration Center (formerly PATRIC), a Bioinformatics Resource Center dedicated to supporting bacterial research. BV-BRC provides comprehensive bacterial genomic data with integrated analysis tools and visualizations. BV-BRC also provides a private workspace where users can upload and analyze their own data. BV-BRC will serve as the platform for the analysis methods covered in this module. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

This lesson provides step-by-step instructions for assembling a genome from a set of bacterial sequence reads using the BV-BRC Genome Assembly Service. Exercises are included to enhance comprehension and build proficiency in using the assembly process. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

This lesson provides step-by-step instructions for annotating a genome from contigs using the BV-BRC Bacterial Genome Annotation Service. Exercises are included to enhance comprehension and build proficiency in using the annotation process. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

This lesson provides step-by-step instructions for assembling, annotating, and performing an automated analysis of a genome from a set of bacterial sequence reads using the BV-BRC Comprehensive Genome Analysis Service. Exercises are included to enhance comprehension and build proficiency in using the service. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

This lesson provides step-by-step instructions for generating a codon-based phylogentic tree from a set of genomes using the BV-BRC Codon Tree Service. Exercises are included to enhance comprehension and build proficiency in using the service. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

This lesson provides step-by-step instructions for finding genomes (and associated taxonomy) in BV-BRC similar to your genome or sequences using the Similar Genome Finder Service. Exercises are included to enhance comprehension and build proficiency in using the service. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

This lesson provides step-by-step instructions for using the BV-BRC Protein Family Sorter to compare presence, absence, and counts of proteins in protein families across a set of genomes. Exercises are included to enhance comprehension and build proficiency in using the tool. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.

This lesson provides step-by-step instructions for using the BV-BRC Proteome Comparison Service to compare a set of genomes against a reference genome, feature group, or FASTA file. Exercises are included to enhance comprehension and build proficiency in using the tool. Note that the exercises were developed using the PATRIC, the predecessor system to BV-BRC. However, BV-BRC was built from PATRIC, so most of the content is still the same.