NEW FALL CLASS: Introductory Bioinformatic’s Laboratory. 3credits

Lecturer: Marcie McClure, Ph.D.

Extension: 7370

Email: mars@parvati.msu.montana.edu

Lectures: Tuesdays 2-3:15pm

Labs: Thursdays 2-5pm

Course number: MB280, enrollment is limited to 20 students

Location: INBRE Bioinformatics Facility, Cooley Hall 2B,

Requirements: It is expected that students will put in an additional 3-5hrs of lab/week as needed. Each student will give a presentation and discussion on the results of their analysis at the end of the semester.

This laboratory covers aspects of Bioinformatics designed to provide students in the biological sciences, (sophomore level standing required), with the necessary skills to perform basic Bioinformatic analyses. Students will be introduced to the notion of different computational platforms and the basic command structure to run programs. An overview of the basic questions and methods in Bioinformatic research, as well as lectures on the specifics of databases, searching, aligning and phylogenetics will be provided. Introductory lectures on micro array analysis and gene expression pathways will also be given.

Tentative syllabus.

8/30/05 1) Introduction to computers and operating languages

• Computer Platforms
• Operating languages
• Command structures
• Programming Concepts

9/1/05 1 st) Lab Assignment: getting to know your machine.

• Know how to access the Internet—send me an email
• Do Unix tutorial

9/6/05 2) Introduction to Bioinformatics-from cell to computer

• databases
• searches
• sequence annotation
• alignments
• phylogenetics
• functional predictions
• structural predictions
• gene expression pathways and micro array data
• math and algorithms

9/8/05 2 nd) Lab Assignment:

• Do a web search for bioinformatics and create list of sites and types of methods.
• Do a conceptual translation of a nucleic acid sequence

9/13/05 3) Database searching and pairwise alignments

9/15/05 3 rd Lab Assignment:

i. Choose a gene family to work on for the rest of the semester

ii. Get an initial sequence

• BLAST to get all gene and protein sequences

9/20/05 4) Multiple alignment and motifs I

9/22/05 4 th Lab Assignment:

• Make a table of %ID, D or S value, sequence size and species distribution.
• Do a literature search on your gene family and read relevant literature.

9/27/05 5) Multiple alignment and motifs II

9/29/05 5 th Lab Assignment:

• Multiple alignment of data-sets (nucleic acid and proteins)
• Manual corrections
• Motif identification

10/4/05 6) Algorithms for searching and aligning sequences

10/6/05 6 th Lab Assignment:

• Continue working on multiple alignment

10/11/05 7 th Molecular Phylogeny I: History, terms, definitions, and limits

10/13/05 7 th Lab Assignment:

• Read the Phylip HTML pages
• Make sure your alignments are ready as input for phylogenetic reconstruction

10/18/05 8 th Molecular Phylogeny II: How to determine a phylogenetic tree

10/20/05 8 th Lab Assignment:

i. Begin reconstruction using Phylip

10/25/05 9 th Molecular Phylogeny III: Improvements and Extensions to Genome Trees

10/27/05 9 th Lab Assignment:

i. Finish phylogenetic reconstruction and interpret data

11/1/05 10 th What can you do with a multiple alignment besides phylogenetics?

11/3/05 10 th Lab Assignment:

• Homology modeling.
• Calculating rates of change

11/8/05 11 th Gene Expression Pathways and Expression Array Analyses

11/10/05 11 th Lab Assignment

i. Demonstration of array analysis.

11/15/05 12 th More Gene Expression Pathways and Expression Array Analyses

11/17/05 lab day to finish projects and work on presentations

11/22/05 lab day to finish projects and work on presentations

NO CLASSES 11/24/05

11/29/05 student presentations

12/1/05 student presentations

12/6/05 student presentations

12/8/05 student presentations