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Foundations of Functional Annotation and Pathway Reconstruction

From Sequence Data to Metabolic Interpretation

Essential Terminology and Evidence Sources

Gene Prediction and Protein Catalog Construction

Principles of Gene Prediction

Selecting and Running Gene Callers

Quality Control Before Functional Annotation

Functional Orthology Mapping with KEGG, COG, and eggNOG

Functional Orthology Mapping Concepts

KEGG Orthology and Pathway Resources

COG Functional Categories

eggNOG-Based Functional Annotation

Reconciling Functional Annotation Results

Pathway Reconstruction and Metabolic Interpretation

From Orthologs to Metabolic Pathways

Assessing Pathway Completeness and Confidence

Reading Metabolic Maps and Biological Scenarios

Pathway Abundance Quantification with HUMAnN

Introduction to HUMAnN

HUMAnN Workflow and Output Tables

Normalization and Comparative Analysis

Interpreting HUMAnN Results Responsibly

Metabolic Network Modeling

Metabolic Networks and Model Components

Draft Model Reconstruction from Annotations

Introduction to Constraint-Based Modeling

Integrated Functional Interpretation Project

Quiz

Gene prediction vs mapping

KEGG KO purpose

Missing gene interpretation

HUMAnN coverage vs abundance

Draft model next steps

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Course Feedback Survey

Unlock the power of genomic and metagenomic data with our comprehensive course, "Principles of Functional Annotation and Metabolic Pathway Reconstruction. " In the rapidly evolving field of bioinformatics and computational biology, translating raw sequence data into meaningful biological insights is a critical skill.

Unlock the power of genomic and metagenomic data with our comprehensive course, "Principles of Functional Annotation and Metabolic Pathway Reconstruction." In the rapidly evolving field of bioinformatics and computational biology, translating raw sequence data into meaningful biological insights is a critical skill. This course provides an in-depth, end-to-end workflow for transforming assembled contigs and sequencing reads into fully reconstructed metabolic pathways and network models.

You will start by mastering the foundations of gene prediction and protein catalog construction, learning how to identify candidate protein-coding regions and perform essential quality control. From there, dive into functional orthology mapping using industry-standard resources like KEGG, COG, and eggNOG. Understand how to confidently assign functions to predicted genes and reconcile complex annotation results.

The journey continues as you learn to reconstruct metabolic pathways, assess pathway completeness, and interpret metabolic maps within biological and environmental contexts. You will also gain hands-on knowledge of pathway abundance quantification using HUMAnN, enabling you to profile gene families from microbial community sequencing data. Finally, the course introduces metabolic network modeling, guiding you through the creation of draft models and the principles of constraint-based modeling. Whether you are a biologist, bioinformatician, or data scientist, this course will equip you with the practical skills and theoretical knowledge to confidently interpret metabolic potential and drive your research forward.

Principles of Functional Annotation and Metabolic Pathway Reconstruction

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            <p>The transformation of genomic and metagenomic sequence data into comprehensive biological interpretations requires a rigorous understanding of functional annotation and metabolic pathway reconstruction. This course provides a systematic exploration of the end-to-end workflow necessary to bridge the gap between raw sequence data and complex metabolic networks. Participants will begin by examining the foundational principles of gene prediction and protein catalog construction, learning to identify candidate protein-coding regions and apply essential quality control measures. Following this, the curriculum delves into functional orthology mapping, utilizing industry-standard resources such as KEGG, COG, and eggNOG to accurately transfer functional information from reference databases to predicted genes while reconciling conflicting or incomplete annotations.</p>

<p>Building upon these functional assignments, the course advances to the reconstruction and interpretation of metabolic pathways. Learners will evaluate pathway completeness, navigate metabolic maps, and quantify pathway abundance using HUMAnN to profile microbial communities from sequencing data. Furthermore, the curriculum introduces the principles of metabolic network modeling, detailing the construction of draft models from annotations and the fundamentals of constraint-based modeling. By synthesizing these methodologies, participants will ultimately execute an integrated functional interpretation project, equipping them with the analytical skills required to evaluate metabolic potential, address evidence gaps, and produce reproducible, high-confidence biological narratives.</p>
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