Genome Wide Characterization Of Gene Family Bioinformatics

Free Download Genome Wide Characterization Of Gene Family Bioinformatics
Published 8/2025
MP4 | Video: h264, 1920x1080 | Audio: AAC, 44.1 KHz
Language: English | Size: 3.86 GB | Duration: 3h 1m
Genome-Wide Characterization of Gene Families: From Sequence to Publication of manuscript
What you'll learn
Define and select a target gene or protein family using databases like Pfam, SMART, and InterPro.
Retrieve genome data and associated annotations from public databases (NCBI, Ensembl, GenBank).
Preprocess and prepare high-quality protein sequence datasets for analysis
Identify homologs using BLAST or HMMER and perform clustering with tools like CD-HIT or OrthoMCL.
Functionally annotate identified sequences using InterProScan, Pfam, and GO terms.
Construct and interpret phylogenetic trees to reveal evolutionary relationships.
Perform optional analyses, including motif conservation, evolutionary rate (dN/dS), and structural analysis
Visualize results with domain architectures, heatmaps, and tree diagrams
Interpret findings in a research context and prepare them for publication
Requirements
Basic understanding of molecular biology and genetics.
Familiarity with protein/gene concepts.
No advanced programming skills required (tools used will be web-based or GUI-based)
Description
Section 1: Introduction & SetupWelcome to the course and a quick orientation to what you'll learn. We will discuss the importance of genome-wide gene family characterization in modern biology, its applications in crop improvement, evolutionary studies, and biotechnology. You will also get an overview of the software, online tools, and databases required for the workflow, along with installation and setup instructions to ensure you're ready to start.Section 2: Defining Your Target Gene/Protein FamilyWe will explore how to clearly define the scope of your study by identifying your target protein family. This includes understanding domain structures using Pfam, SMART, and InterPro, and how these platforms help you recognize conserved motifs and functional domains. You'll learn why domain knowledge is crucial before data collection.Section 3: Data Retrieval & PreparationHands-on steps to download genome assemblies from NCBI, Ensembl, or GenBank, followed by cleaning raw data and extracting high-quality protein sequences. We'll cover naming conventions, metadata organization, and preparation tips to ensure smooth downstream analyses.Section 4: Homology Search & ClusteringLearn how to perform BLAST and HMMER searches to detect homologous sequences. You'll understand how to cluster sequences with CD-HIT or OrthoMCL, reduce redundancy, and validate dataset integrity before analysis.Section 5: Functional AnnotationUse InterProScan and Pfam for function prediction, and assign GO terms for biological interpretation. You'll see how annotation links sequence data to biological roles and potential experimental targets.Section 6: Phylogenetic AnalysisPerform multiple sequence alignments (MSA) with MAFFT or Clustal Omega, then construct phylogenetic trees using FastTree, RAxML, or PhyML. We will also discuss how to interpret evolutionary relationships and lineage-specific expansions.Section 7: Optional Advanced AnalysesGo beyond the basics with motif discovery, evolutionary rate calculations (dN/dS), and structural modeling of proteins. These approaches can reveal adaptive evolution, structural constraints, and functional divergence.Section 8: Visualization & ReportingLearn to create domain architecture diagrams, generate high-quality phylogenetic tree visuals, and produce heatmaps for publication-ready figures. We'll share tips to make your visuals compelling for journals and conferences.Section 9: Conclusion & Next StepsWrap up by revisiting the complete workflow, exploring real-world applications in crop genetics and functional genomics, and receiving guidance on how to integrate these skills into your future research and career development.
This course is designed for anyone interested in exploring genomes and uncovering the diversity, structure, and evolution of gene families. You will find this course valuable if you are: Graduate or postgraduate students in molecular biology, genetics, plant sciences, or bioinformatics who want to gain practical skills in genome-wide characterization. Researchers aiming to analyze and annotate gene or protein families for their publications or thesis work. Lab professionals and technicians seeking to expand their bioinformatics toolkit without deep coding knowledge. Early-career scientists preparing for research collaborations or postdoctoral projects involving genomics. Biotech and agriculture professionals working on crop improvement, functional genomics, or breeding programs. Whether you are looking to apply these skills to plants, animals, microbes, or other organisms, this step-by-step course will equip you with the tools and workflow to perform high-quality genome-wide analyses and confidently interpret your results.

Homepage