ITCS 6010
METHODS IN BIOINFORMATICS
Class Time: Tuesday-Thursday 2:00p.m.-3:20p.m.
Kennedy 236 Fall 2004
Instructor: Dr. Lawrence Mays Office: Kennedy 223
Office Phone: (704)-687-6010 Office Hours: Tuesday and Thursday
Email: lemays@uncc.edu 3:30 to 4:30
Bioinformatics is the discovery, development and application of powerful computational tools to extract knowledge from complex biological data. This approach has joined theory and experiment to become a major tool for biological discovery. The course will explore the use of computers in the analysis of genomic, proteomic, and gene expression datasets. Specifically, the PERL programming language will be used to solve a number of otherwise difficult problems in computational biology. No prior knowledge of PERL, bioinformatics, genetics, biochemistry, or cell biology is assumed; you will learn what you need to know in this class.
Course Requirements and Expectations:
1) Attend all class meetings.
2) All projects and assignment should be turned in on time.
3) Do not have cell phones, papers or any noise-making device active during class time; it is distracting both to you, and those around you. If you have an emergency and must leave such a device on, it must be set to silent or vibrate.
4) Academic Integrity: All UNCC students have the responsibility to be familiar with and to observe requirements of the UNCC Code of Student Academic Integrity (refer to www.uncc.edu/policystate/ps-105.html). This code forbids cheating, fabrication or falsification of information, multiple submissions of academic work, plagiarism, abuse of academic materials (such as library books on reserve), a complicity in academic dishonesty.
Grades:
25% midterm exam; 40% participation, projects, and class assignments;
35% final exam. Each student will work on an individual project and report on it during the last 2 weeks of class. The project proposals will be presented (10 min each) on 10/26/04.
A: 90%-100%
B: 80%-89%
C: 70%-79%
Recommended Text: Beginning PERL for Bioinformatics, James Tisdall, O’Reilly,
2001 (Available from Amazon.com and on-line). For students with no background in Perl, see Beginning Perl, by Cozens (http://learn.perl.org/library/beginning_perl/).
For a good overview of molecular biology for computer scientists, see Chapter 1 of Hunter (http://www.aaai.org/Library/Books/Hunter/hunter.html).
Teaching Assistant: Gao Zhang
Office: 234-A Kennedy
E-mail address: gzhang5@uncc.edu
Lab Facilities: Most programming exercises will use PERL, and can be done by logging onto the Apple Biocluster (ssh yourname@coitapple01.uncc.edu). I will establish accounts for all students. Perl is also found on nearly all UNIX/LINUX/SOLARIS workstations and on MAC OS X or it can be installed free on Windows computers. Later exercises will require Bioperl, which is present on the Biocluster and can be loaded onto non-MOSAIC computers running Perl (www.bioperl.org).
Date Topic
8/24 Introduction to Bioinformatics; the future of bioinformatics. Introduction to Perl. Setting up user accounts.
8/26 The meaning of life; structure of DNA; replication. Amino acids and proteins. How to read DNA and protein sequences. Palindromes. Assignment: Write your first Perl program: the reverse complement. Cozens, Chapters 1-4. Hunter pp 1-5 (up to sec 1.2). See Presentation
8/31 The Central Dogma. From DNA to protein. Transcription and translation. The genetic code. ORF. Computing protein sequences from DNA (simple version). Assignment: Perl program to transcribe DNA to RNA. Cozens, Chapter 5 & Appendix A. See Presentation
9/2 From DNA to protein, continued. Perl program to translate RNA to amino acid sequence. Characteristics of Prokaryotes. Assignment: write simple ORF finder for prokaryotic DNA. SeePresentation
9/7 Eukayotes. Exons, introns, splicing (alternative and otherwise), snRNPs, junk DNA.
9/9 Eukaryotes continued. Interpreting the databases. GT-AG rule.
9/14 No class
9/16 Using nucleotide databases.
9/21 Working with DNA; restriction maps, ORFs, exons, genes, assembling fragments.
9/23 Using protein and specialized sequence databases.
9/28 Working with a protein sequence; predicting physical and functional properties. Using SwissProt to look up a protein. Data formats. More Bioperl.
9/30 Sequence similarity; BLAST. BLAST a protein. Reading the BLAST output. Global alignment: Needleman-Wunsch. Local alignment: Smith-Waterman.
10/5 Getting started with Bioperl: Reading and writing a GenBank entry.
Bioperl BLAST.
10/7 More BLAST. Multiple alignments and ClustalW.
10/12 Fall Break No Classes
10/14 Mid-term
10/19 No Class
10/21 No Class
10/26 Student presentations of proposals.
10/28 Object-oriented programming in Perl
11/2 Bioperl modules.
11/4 More Bioperl.
11/9 Genetic recombination; SNPs; Haplotypes; Jumping Genes.
11/11 Finding restriction sites in DNA sequences.
11/16 Introduction to 3-D protein structures.
11/18 3-D Protein structures (con’t).
11/23 Working with RNA.
11/25 Thanksgiving Break: No Class
11/30 Student presentations.
12/2 Student presentations.
12/7 Last Class Day: Student presentations (if needed).
12/9 Reading Day/No Classes
Final Exam Monday December 13, 2004 3:30p.m. To 6:30p.m.