Nucleotide Sequence Analysis Course Description

Course: 11:126:483 Nucleotide Sequence Analysis (3 credits)

Normally Offered: Fall and winter terms by Dr. Gerben J. Zylstra

Pre-requisites and other registration restrictions:
The prerequisite for Nucleotide Sequence Analysis is one of the following courses:
11:115:404 General Biochemistry
11:126:481 Molecular Genetics
11:126:427 Methods in Recombinant DNA
Students must be familiar with DNA structure, restriction enzymes, general cloning technology, DNA sequencing, transcription and translation, and general gene and operon structure. Students should have a working knowledge of PC computers.

Format: One three-period computer laboratory per week. Fridays 8:10 to 12:50 in the Biotechnology, Animal Science, and Chang Library Computer Teaching Laboratory, 124 Foran Hall.

Description: This is a computer laboratory course that utilizes various PC and web-based programs for the analysis of nucleotide and amino acid sequences. The course serves as an advanced elective in both the Biotechnology and Biochemistry majors and satisfies the general computer competence requirement. The course is highly recommended for students interested in a career in biotechnology, biochemistry, or molecular biology.

The course introduces students to the methods of analyzing DNA sequences and the use of sequence information available in international databases. The course covers analysis of primary data obtained from DNA sequencers, assembly of raw data into a contiguous sequence, finding open reading frames, translating nucleotide sequences into amino acid sequences, determining protein and DNA characteristics, identifying genes and proteins by database searches, determining which database searching method to use (blastN, blastP, blastX, etc.), motif searches to identify amino acid signature sequences, searching for and downloading sequences from the GenBank database, importing and interconversion of sequences, aligning sequences, calculating and drawing phylogenetic trees, and genome analysis.

Special emphasis is placed on the application of computer programs to answering questions about nucleotide and amino acid sequences. Each week of the course will introduce a new method of sequence analysis through a laboratory exercise. A series of practical problems will then be solved. Each week builds on information learned in previous exercises.

Examinations: Two 2-hour examinations are given during the laboratory period at one-third and two-thirds the way through the course. The exams are open book/notes, problem-solving, timed tests. A final written project report is due at the end of the term in place of a final exam.

Other Requirements: Many of the required readings and other course materials are available only on-line or in the help files of the computer programs. Students are encouraged to purchase a zip disk to store the data for the lab exercises.

Additional Information: Visit the course home page to view a recent syllabus.