Bioinformatics and Gene Sequence Analysis

Course Number: 
PABIO 536
Course Type: 
Methods
Currently Offered: 
Yes
Credits: 
3
Quarter: 
Spring
Meeting Time: 
MW 1000-1120
Location: 
UW
Instructor (MCB Faculty): 
Rose, Timothy
Course Description: 

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.

Learning Objectives: 

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.  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.
Required Text: 
Although there is no required text-book, "Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Baxevanis AD and Ouellette BF 2nd ed. (2001), Wiley Interscience, New York", available at the University Bookstore, South Campus Center for $65, may be helpful. On-line access to most other reading material is available on the class Web site (Reading List). Computers for student use are available in the Health Sciences Library Learning Commons.
Course requirements, examinations and grading: 

1). Weekly homework assignments will consist of sequence analysis problems. Assignments will be due by email to bioinfo@u.washington.edu by 5pm the Friday of each week. Grades for each assignment will drop 1.0 unit for each week late.  If extra credit problems are given, the extra points can raise the homework grade to the maximum 4.0. 

2) A take-home final will be given.  This final is to be done individually with no collaboration with others.

3). 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.  Collaborating on the homework is encouraged but the work must be done individually.  The take-home final is not collaborative and must be done individually.

Lectures and computer labs will be held in the Health Sciences Library Learning Commons Classroom C from 10:00-11:20 AM. These will be part lecture, part hands-on exercises. We will be using PCs running Windows.

HOME PAGE: http://courses.washington.edu/bioinfo/
EMAIL:bioinfo@u.washington.edu

Sample Schedule:

 

Week 1

April 1

The nature of biological sequences

Introduction/Lecture

 

April 3

NCBI resources and databases

Lecture/Lab

 

April 5

HW due

 

Week 2

April 8

NCBI resources

DNA analysis

HW Discussion

Lecture/Lab

 

April 10

DNA analysis

Lab

 

April 12

HW due

 

Week 3

April 15

DNA analysis

Protein analysis

HW Discussion

Lecture/Lab

 

April 17

Protein analysis

Lab

 

April 19

HW due

 

Week 4

April 22

Protein analysis

BLAST searching – Nucleotide BLAST

HW Discussion

Lecture/Lab

 

April 24

Nucleotide BLAST

Lab

 

April 26

HW due

 

Week 5

Apr 29

Nucleotide BLAST

Protein BLAST

HW Discussion

Lecture/Lab

 

May 1

Protein Motifs

Lecture/Lab

 

May 3

HW due

 

Week 6

May 6

Protein BLAST

EST/Gene structure

HW Discussion

Lecture/Lab

 

May 8

EST/Gene structure

Lab

 

May 10

HW due

 

Week 7

May 13

EST/Gene structure

SNP analysis

HW Discussion

Lecture/Lab

 

May 15

SNP analysis

Lecture/Lab

 

May 17

HW due

 

Week 8

May 20

SNP analysis

Multiple sequence alignment

HW Discussion

Lecture/lab

 

May 22

Phylogenetic analysis                            Take-home finals distributed

Lecture/lab

 

May 24

HW due

 

Week 9

May 27

Memorial Day

 

 

May 29

Phylogenetic analysis

Protein structure

HW Discussion

Lecture/lab

 

May 31

HW due

 

Finals

June 5

Take-home finals due

 

Week

   

 

Areas of Interest: 
Gene Expression, Cell Cycle & Chromosome Biology
Areas of Interest: 
Genetics, Genomics & Evolution
Methods Area: 
Cancer Biology
Cell Signaling & Cell/Environment Interactions
Gene Expression, Cell Cycle & Chromosome Biology
Microbiology, Infection & Immunity
Molecular Structure & Computational Biology