This Bioinformatics course offers students a unique opportunity to explore cutting-edge techniques and tools essential for modern biological research. This beginner-friendly course is the perfect starting point! It introduces fundamental concepts and tools, guiding you step-by-step through topics like sequence retrieval, BLAST, multiple sequence alignment, and phylogenetic tree construction.
By the end of this course, you’ll gain hands-on experience with essential bioinformatics techniques and be prepared to explore more advanced topics. Whether you’re a student, researcher, or enthusiast, this course provides the foundational knowledge to help you succeed in the rapidly growing field of bioinformatics.
Course contents
Week 01 : Introduction to Bioinformatics
- Overview:
- Definition and scope of Bioinformatics.
- Applications in biology, medicine, and agriculture.
- Key Concepts:
- Biological databases (NCBI, EMBL, UniProt).
- Basic terminologies: genes, proteins, genomes.
- Hands-On:
- Introduction to online bioinformatics tools and resources.
- Navigating biological databases.
Week 02 : Sequence Retrieval
- Overview:
- Types of biological sequences (DNA, RNA, Protein).
- Understanding FASTA and GenBank formats.
- Key Concepts:
- Accession numbers, annotations, and metadata.
- Tools for sequence retrieval (NCBI Entrez, UniProt).
- Hands-On:
- Retrieving sequences using NCBI Entrez.
- Saving and visualizing sequences in FASTA format.
Week 3: Basic Local Alignment Search Tool (BLAST)
- Overview:
- Introduction to sequence alignment.
- Types of BLAST (blastn, blastp, blastx, tblastn).
- Key Concepts:
- Scoring matrices (BLOSUM, PAM).
- E-value, bit score, and alignment significance.
- Hands-On:
- Running BLAST queries on NCBI.
- Interpreting BLAST results.
Week 4: Multiple Sequence Alignment (MSA) and Phylogenetic Tree Construction
- Multiple Sequence Alignment:
- Importance of MSA in bioinformatics.
- Tools for MSA (Clustal Omega, MUSCLE).
- Evaluating MSA quality.
- Phylogenetic Tree Construction:
- Principles of phylogenetics.
- Types of trees (rooted, unrooted).
- Tools (MEGA, PhyML).
- Hands-On:
- Performing MSA using Clustal Omega.
- Constructing a phylogenetic tree from aligned sequences.
Week 5: Domain and Motif Identification
- Overview:
- Importance of domains and motifs in proteins.
- Databases for domain/motif identification (Pfam, PROSITE).
- Key Concepts:
- Conserved regions and their biological significance.
- Regular expressions in motif finding.
- Hands-On:
- Identifying domains using Pfam.
- Discovering motifs with PROSITE.
Course Outcome
By the end of this course, participants will:
- Understand the fundamental concepts of bioinformatics.
- Retrieve and analyze biological sequences.
- Perform sequence alignment and construct phylogenetic trees.
- Identify functional domains and motifs in proteins.