Week 3 — Extended Module
Week 3 — Extended Module
Duration
15 hours (internationally recognized)
3 Days
certificate
Accredited Innovation Training Program (AInTP) ®
Location
iGene Medical Training & Research Center
Date
This course runs from Sep 21th, 2025, to Sep 23th, 2025
Who is this course for?
- Comparative genomics/evolution enthusiasts.
- Researchers needing reliable alignments for phylogeny, structure, or primer/probe design.
- Students preparing figures for reports or posters.
A hands-on, step-by-step journey from the fundamentals to applied analysis. Trainees learn how to retrieve and clean real sequence data, run core DNA/protein analyses, build high-quality alignments, and generate publication-ready outputs. Each week delivers ~15 training hours (internationally accredited, AInTP) with practical exercises and instructor feedback.
Week 3 — Extended Module
What you gain (brief): High-quality pairwise/multiple alignments and clear visualizations suitable for downstream structural/evolutionary analysis.
-
Day 1: Pairwise and Multiple Sequence Alignment (5 hours)
- Lecture (2 hours):
- Dot plots for sequence comparison.
- Local vs. Global alignment (Lalign).
- Introduction to Multiple Sequence Alignment (MSA) and its applications.
- Progressive alignment methods: The logic behind ClustalW.
- Practical (3 hours):
- Creating and interpreting dot plots.
- Performing a multiple sequence alignment with ClustalW and T-Coffee.
Day 2: Editing and Publishing Alignments (5 hours)
- Lecture (2 hours):
- Recognizing and converting different alignment formats (FASTA, MSF, ALN).
- Visualizing and editing alignments with Jalview.
- Creating publication-quality figures with Boxshade and Logos.
- Practical (3 hours):
- Using online tools to convert alignment formats.
- Editing an alignment in Jalview: Removing Gaps and Grouping Sequences.
- Generating a shaded alignment with Boxshade.
Day 3: Structures and Phylogenetics
- Introduction to Structural Bioinformatics (5 hours)
- Lecture (2 hours):
- From primary to 3D structure.
- Retrieving and viewing structures from the Protein Data Bank (PDB).
- Predicting secondary structure (PSIPRED).
- Practical and Tasks (3 hours):
- Using the PDB to find and visualize a protein structure.
- Predicting the secondary structure of a protein and interpreting the results.
- Group task: Create a high-quality, well-annotated multiple sequence alignment for a given protein family.
Target audience
-
Comparative genomics/evolution enthusiasts.
-
Researchers needing reliable alignments for phylogeny, structure, or primer/probe design.
-
Students preparing figures for reports or posters.