Bioinformatics: Course content (MLBI-512)

Course Outline

            Analyzing Protein Sequences

• A brief history of sequence analysis
• Reading protein sequences from N to C
• Retrieving protein sequences from databases
• Computing amino-acid composition, molecular weight, isoelectric point
• Computing how hydrophobic or hydrophilic a protein is, predicting antigenic sites,
• Predicting elements of secondary structure
• Predicting the domain organization of proteins
• Visualizing protein structures in 3-D
• Predicting a protein’s 3-D structure from its sequence
• Finding all proteins that share a similar sequence
• Classifying proteins into families
• Finding the best alignment between two or more proteins
• Finding evolutionary relationships between proteins, drawing proteins’ family trees
• Use of ExPASy

            Analyzing DNA Sequences

• Reading DNA sequences the right way
• Retrieving DNA sequences from databases
• The two sides of a DNA sequence
• Palindromes in DNA sequences

Analyzing RNA Sequences

• RNA structures: Playing with sticky strands

DNA Coding Regions

• Translating DNA into proteins

Miscellaneous

• Computing nucleotide compositions Identifying restriction sites
• Designing polymerase chain-reaction (PCR) primers
• Identifying open reading frames (ORFs)
• Predicting elements of DNA/RNA secondary structure
• Finding repeats
• Computing the optimal alignment between two or more DNA sequences
• Finding polymorphic sites in genes
• Assembling sequence fragments

                Working with Entire Genomes

• The Ensembl project

Similarity Searches on Sequence Databases

• BLAST

Use of Pubmed/Medline