Timothy M Rose
Nature and relevance of molecular sequence information, computer-based protein, and DNA sequence analysis, molecular sequence and genomic databases, and methods for database accession and interrogation. Prerequisite: background in molecular biology and permission of instructor. Offered: jointly with PABIO 536/PHG 536; Sp.
This course is a joint offering of the Graduate Program in Pathobiology, the 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.
Student learning goals
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.
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
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.
Describe the basics of amino acid substitution in proteins with regard to structural and functional outcomes in both mutational and evolutionary studies
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. 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.
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. 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.
General method of instruction
The course will be given as a series of lectures and hands-on computer labs.
A strong background in molecular biology, cell biology and biochemistry is recommended.
Class assignments and grading
Weekly homework assignments will consist of sequence analysis problems. A take-home final will be given. This is a graded class with an option for Credit/No-Credit; Grades will be determined from the homework (2/3) and final (1/3). Grading will be on the 4.0 scale and you must obtain a 2.7 to get credit.
Grades are assigned on the basis of completed homework assignments with extra credit possibilities.