4.8
étoiles
24 évaluations

Rebecca Wattam

2 858 déjà inscrits

Offert par

Bacterial Bioinformatics

Université de Virginie

À propos de ce cours

10 594 consultations récentes

This course provides demonstrations and exercises for performing common genomics-based analysis tasks of bacterial sequence data.  It uses PATRIC, the PathoSystems Resource Integration Center, as the platform for analysis. PATRIC is the NIH/NIAID-funded bacterial Bioinformatics Resource Center, providing comprehensive bacterial genomic data with integrated analysis tools and visualizations. PATRIC also provides a private workspace where users can upload and analyze their own data. 
Course participants will gain skills needed to do comparative analysis of bacterial genomes, starting with raw sequence data.The lessons in the first module cover genome assembly, annotation, phylogenetic tree construction, and protein family / proteome comparisons. Each lesson builds on the previous, creating a complete baseline analysis workflow.

Dates limites flexibles

Réinitialisez les dates limites selon votre disponibilité.

100 % en ligne

Commencez dès maintenant et apprenez aux horaires qui vous conviennent.

Niveau intermédiaire

This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.

Approx. 14 heures pour terminer

Anglais

Sous-titres : Français, Portugais (européen), Russe, Anglais, Espagnol

Ce que vous allez apprendre

Learn how to assemble a bacterial genome

Learn how to annotate a bacterial genome

Learn how to generate a phylogenetic tree from a set of bacterial genomes

Learn how to perform basic comparative analyses of a set of bacterial genomes

Dates limites flexibles

Réinitialisez les dates limites selon votre disponibilité.

100 % en ligne

Commencez dès maintenant et apprenez aux horaires qui vous conviennent.

Niveau intermédiaire

This class is geared towards biologists, bacteriologists, and bioinformaticians with a basic knowledge of comparative genomics.

Approx. 14 heures pour terminer

Anglais

Sous-titres : Français, Portugais (européen), Russe, Anglais, Espagnol

Enseignant

Évaluation de l'enseignant

4,78/5 (15 notes)

Rebecca Wattam

Professor

Biocomplexity Institute and Initiative

2 858 étudiants

1 cours

Offert par

Université de Virginie

A premier institution of higher education, The University of Virginia offers outstanding academics, world-class faculty, and an inspiring, supportive environment. Founded by Thomas Jefferson in 1819, the University is guided by his vision of discovery, innovation, and development of the full potential of students from all walks of life. Through these courses, global learners have an opportunity to study with renowned scholars and thought leaders.

Programme du cours : ce que vous apprendrez dans ce cours

Semaine

Semaine 1

1 heure pour terminer

Introduction

This lesson provides an introduction to PATRIC, the PathoSystems Resource Integration Center, a Bioinformatics Resource Center dedicated to supporting bacterial research. PATRIC provides comprehensive bacterial genomic data with integrated analysis tools and visualizations. PATRIC also provides a private workspace where users can upload and analyze their own data. PATRIC will serve as the platform for the analysis methods covered in this module.

1 heure pour terminer

7 vidéos (Total 42 min)

Semaine

Semaine 2

1 heure pour terminer

Assembly

This lesson provides step-by-step instructions for assembling a genome from a set of bacterial sequence reads using the PATRIC Genome Assembly Service. Exercises are included to enhance comprehension and build proficiency in using the assembly process.

1 heure pour terminer

7 vidéos (Total 49 min)

7 vidéos

Introduction to genome assembly6 min

Uploading read files to the workspace for assembly11 min

Submitting reads to the Genome Assembly Service8 min

Selecting assembly strategies and submitting the assembly job8 min

Monitoring the assembly job and reviewing job results7 min

Genome coverage in Genome Report2 min

Assembly questions and getting help with problems4 min

1 exercice pour s'entraîner

Review of genome assembly30 min

Semaine

Semaine 3

2 heures pour terminer

Annotation

This lesson provides step-by-step instructions for annotating a genome from contigs using the PATRIC Genome Annotation Service. Exercises are included to enhance comprehension and build proficiency in using the annotation process.

2 heures pour terminer

7 vidéos (Total 77 min)

7 vidéos

Introduction to genome annotation in PATRIC5 min

Uploading contig files to the PATRIC workspace12 min

Submitting a job to the PATRIC Genome Annotation Service7 min

Reviewing the resulting Genome Report19 min

Downloading the generated files 11 min

Viewing your annotated genome in PATRIC15 min

Finding help or reporting problems with the service5 min

1 exercice pour s'entraîner

Review of genome annotation30 min

Semaine

Semaine 4

2 heures pour terminer

Comprehensive Genome Analysis

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 PATRIC Comprehensive Genome Analysis Service. Exercises are included to enhance comprehension and build proficiency in using the service.

2 heures pour terminer

10 vidéos (Total 101 min)

Semaine

Semaine 5

2 heures pour terminer

Codon-Based Phyogenetic Trees

This lesson provides step-by-step instructions for generating a codon-based phylogentic tree from a set of genomes using the PATRIC Codon Tree Service. Exercises are included to enhance comprehension and build proficiency in using the service.

2 heures pour terminer

9 vidéos (Total 107 min)

9 vidéos

Introduction to codon trees2 min

Creating genome groups for building codon trees16 min

Submitting the tree-building job11 min

Reviewing the codon tree report11 min

Accessing codon tree files in the jobs folder10 min

Removing problem genomes from groups 17 min

Using the Protein Family Sorter to improve the tree16 min

Viewing the tree in FigTree8 min

Finding help and citing PATRIC11 min

1 exercice pour s'entraîner

Review of codon trees30 min

Semaine

Semaine 6

1 heure pour terminer

Similar Genome Finder

This lesson provides step-by-step instructions for finding genomes (and associated taxonomy) in PATRIC 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.

1 heure pour terminer

4 vidéos (Total 25 min)

Semaine

Semaine 7

2 heures pour terminer

Protein Family Sorter

This lesson provides step-by-step instructions for using the PATRIC 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.

2 heures pour terminer

13 vidéos (Total 99 min)

13 vidéos

Introduction to Protein Family Sorter4 min

Using Global Search7 min

Creating a genome group5 min

Submitting a Protein Family Sorter Service analysis job6 min

Protein Family Sorter tabular results7 min

Filtering tabular results8 min

Heatmap filtering5 min

Heatmap clustering5 min

Anchoring and downloading heatmap data8 min

Using the Feature Table and Compare Region Viewer14 min

Downloading sequences from Feature Table and viewing in the Genome Browser11 min

BLASTing a genomic region10 min

Protein Family Sorter summary2 min

1 exercice pour s'entraîner

Review of Protein Family Sorter30 min

Semaine

Semaine 8

2 heures pour terminer

Proteome Comparison

This lesson provides step-by-step instructions for using the PATRIC 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.

2 heures pour terminer

11 vidéos (Total 74 min)

11 vidéos

Introduction to Proteome Comparison4 min

Selecting parameters8 min

Selecting a reference genome3 min

Using a feature group or FASTA file as input6 min

Using a feature group as the reference2 min

Using a FASTA file as the reference4 min

Selecting the genomes to use for the comparison3 min

3 flavors of reference genomes5 min

Reviewing the output job results21 min

Citing PATRIC and getting help5 min

Summary of analysis of two assembly strategies8 min

1 exercice pour s'entraîner

Review of Proteome Comparison30 min

Avis

4.8

7 avis

5 stars
83,33 %
4 stars
12,50 %
3 stars
4,16 %

Meilleurs avis pour BACTERIAL BIOINFORMATICS

par PP23 déc. 2020

very useful course , can solve a lot of problem in bacterium genome analysis easily

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Bacterial Bioinformatics

Bacterial Bioinformatics