PHG 536 - Bioinformatics and Gene Sequence Analysis

Alternate Course Number 


Course Description 

This course is a joint offering of the Department of Pathobiology , Department of Medical Education and Biomedical Informatics and the Institute of Public Health Genetics. It forms part of the curriculum for the Ph.D. program in Pathobiology and the M.S. program in Genetic Epidemiology, Institute of Public Health Genetics, and is open to students and postgraduate trainees in the biomedical, computer, and information sciences. Students are expected to learn key concepts and skills in the accumulation, analysis, and retrieval of biological sequence information in the context of computer-based informatics, the Internet, and world-wide databases. 

Course Objectives 

At the end of this course, the student should be able to:

  1. Describe the basic nucleotide building blocks of DNA and how to detect the presence of important features such as stem-loop structures and complementary DNA.
  2. Describe the basic amino acid building blocks of protein sequences and how these building blocks contribute to structure and function
  3. Demonstrate a working knowledge of the relevant protein, DNA and genomic databases at the National Center for Biotechnology Information and other centers, including record analysis, data archiving and search strategies.
  4. Demonstrate a working knowledge of basic DNA sequence analysis tools and their applications, including restriction site analysis, DNA translation, open reading frame analysis, primer prediction, pair-wise alignments, sequence assembly, nucleotide frequencies, multiple sequence alignment, pattern matching, and dot-matrix analysis.
  5. Demonstrate a working knowledge of basic protein sequence analysis tools and their applications, including motif searching, pattern matching, amino acid frequencies, molecular weight and isoelectric point determinations, hydrophobicity, hydrophilicity, amphipathicity and secondary structure prediction.
  6. Describe the basics of amino acid substitution in proteins with regard to structural and functional outcomes in both mutational and evolutionary studies.
  7. Demonstrate the use of available tools and databases to identify the important structural elements of a complex gene, including sequence motifs, exons, introns, coding, non-coding and regulatory regions.
  8. Demonstrate the use of available tools and databases to decipher the structural elements of a complex protein, including conserved motifs, maturation sites, signal peptides, transmembrane domains, secondary structural domains and tertiary protein structure.
  9. Demonstrate a working knowledge of the basics of BLAST similarity searches, multiple sequence alignment, and phylogenetic analysis and their use in DNA and protein sequence comparisons.
  10. Describe the basics of gene and protein evolution and how available bioinformatic tools can be used to ascertain gene relationships, including similarity, homology, orthology and paralogy.

Example Syllabus 

Quarter(s) Offered 



Background in molecular biology and permission of instructor

Fundamental Areas of Study 

Human Genetics