Foundations of Bioinformatics

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Foundations of Bioinformatics: From Sequences to Insights

Overview:

This intensive five-day training program provides a comprehensive introduction to bioinformatics, equipping participants with both the theoretical background and practical skills needed to analyze biological data. Starting from fundamental concepts such as the central dogma and biological databases, the course progresses through sequence alignment, phylogenetics, genomics, transcriptomics, and protein bioinformatics. By combining lectures with hands-on exercises, participants will gain confidence in using widely adopted bioinformatics tools and databases to address real-world biological questions.

Workshop Structure:

Duration: 5 Days
Session Format: Every session consists of approximately 2 hours of theoretical lectures and 2–3 hours of guided practical training.
Location: Live Online Sessions (Zoom)
Certification: Certificate of Completion Provided

Key Learning Outcomes:

By the end of this course, participants will be able to:

Explain the principles, history, and applications of bioinformatics.
Navigate and retrieve data from major bioinformatics databases (NCBI, Ensembl, UniProt, etc.).
Perform pairwise and multiple sequence alignments and interpret phylogenetic trees.
Explore genomic data using genome browsers and perform basic variant analysis.
Explore transcriptomic analysis to identify differentially expressed genes.
Design primers using established online tools and validate their specificity.
Annotate proteins functionally and structurally using public resources.
Visualize and interpret molecular structures for functional insights.

Day-by-Day Breakdown:

Day 1: Foundations of Bioinformatics & Biological Databases:

Theory:

What is bioinformatics? Definition, history, and applications.
Central dogma & molecular data types (DNA, RNA, proteins).
Types of biological data: sequences, structures, literature.
Overview of major bioinformatics databases (NCBI, EMBL-EBI, Ensembl, UniProt, PDB, PubMed).

Practical:

Navigating NCBI, EMBL, Ensembl, and UniProt.
Retrieving nucleotide and protein sequences (example: BRCA1).
Downloading data in FASTA, GenBank formats.
Searching PubMed for relevant research articles.
Interpreting basic database entries.

Day 2: Sequence Analysis, Alignment & Phylogenetics

Theory:

Introduction to sequence analysis: purpose and methods
Pairwise alignment: global vs. local (Needleman–Wunsch, Smith–Waterman)
Multiple Sequence Alignment (MSA) basics: Clustal Omega, MUSCLE
Introduction to phylogenetics: rooted vs. unrooted trees, cladograms vs. phylograms
Basics of tree construction: distance-based vs. character-based methods

Practical:

Performing pairwise sequence alignment using NCBI BLAST.
Conducting MSA with Clustal Omega & MUSCLE ((via EMBL-EBI or MEGA).
Building a phylogenetic tree using MEGA or PhyloT.
Exercise: compare evolutionary relationships of orthologous genes.

Day 3: Genomics, Genome Browsers & Variant Analysis

Theory:

Genome structure, annotation and formats (GTF/GFF, BED).
Basics of genome sequencing, assembly, and annotation.
Introduction of NGS data.
SNPs, CNVs, and regulatory regions.
Human Genome Project and its impact.

Practical:

Exploring UCSC Genome Browser & Ensembl Genome Browser.
Annotating a DNA sequence: identifying exons, introns, and regulatory elements.
Using dbSNP or Ensembl Variation for variant analysis.
Using gene prediction tools (GENSCAN, ORF Finder).
Optional: Viewing genomic data with IGV.

Day 4: Transcriptomics & Primer Design

Theory:

Introduction to transcriptomics (microarray vs RNA-seq).
Basics of normalization and differential expression analysis.
Primer design principles: melting temperature, GC content, specificity, product size.

Practical:

Analyzing real datasets using GEO2R.
Identifying differentially expressed genes
Designing primers using NCBI Primer-BLAST and Primer3.
Validating primer specificity using BLAST.

Day 5: Protein Bioinformatics, Functional Annotation & Structural Analysis

Theory:

Protein structure levels (primary to quaternary).
Protein motifs and domains.
Functional annotation: Gene Ontology (GO), KEGG pathways.
Introduction to 3D structure prediction & homology modeling
Basics of molecular docking

Practical:

Using UniProt, Pfam, InterPro for protein annotation
Predicting protein properties with ExPASy ProtParam
Visualizing protein structures with PyMOL or Chimera
Running a homology modeling demo with SWISS-MODEL or Phyre2
Final integrative mini-project: from sequence retrieval → alignment → annotation → structure → phylogeny

Target Audience :

Graduate students, researchers, and professionals in life sciences who are new to bioinformatics.
Laboratory scientists looking to incorporate bioinformatics into their research workflows.
Computational scientists seeking to understand biological data analysis.

Prerequisites :

Familiarity with using a computer and navigating the internet.
No prior experience in bioinformatics is required, but some exposure to molecular data will be helpful.