Bioinformatics and Genome Analysis - Spring 1998

CHEM 451/EPWS 451/ MOLB550

Bioinformatics and Genome analysis

SYLLABUS Spring 1998

The amount of DNA sequence data being collected today is increasing rapidly and there is no end in sight, given the limits of current technology and the huge diversity of life on earth. It has never been more important than now for biologists to be trained in information technology and computational science, not just because the job market is good, but also because the discoveries yet to be made are tremendously exciting. This course will introduce the basic concepts of the discipline of bioinformatics and introduce basic computational tools and methods that are used in the string organizing and analysis of data. It will include an introduction to large scale DNA sequencing methods, and the methods and algorithms used to perform analyses such as alignments, homology searches and advanced searching techniques. In addition the course will present basic computational tools such as the Perl language and basic file handling and database concepts.

Please note that if you have or think you may have a disability that interferes with your academic progress, you may contact Services for Students with Disabilities at 646-6840 (voice) or 646-1918 (TTY) for an appointment. Services for Students with Disabilities is located in Garcia Annex, Room 102. Current and appropriate documentation will be required in order to receive services.

Grading: There will be two in-class exams; one at mid-term and one final exam worth 40 % of the grade. In addition, there will be three graded projects worth 60% of the grade.

Instructors: Dr Peter Lammers (Chem & Biochem Rm W371) x 6-3918 plammers@nmsu.edu

Dr. Craig Liddell (Gerald Thomas Building room GT233) x 6-4110 craig@taipan.nmsu.edu.

Lectures/ Laboratory: Chemistry 201 - W 02:30 - 5:30

Required Reference: Schwartz, R.L. (1993) Learning Perl. O'Reilly & Associates Inc.

Timetable, Lectures and Assignments, and examination schedule for the course:

Week	Lecturer	Date(s)	Topic	Web Sites	References and Assiged Readings
1	PL	Jan 14	Introduction: Structural and Functional Genomics & DNA Sequencing Overview	None
2	PL	Jan 21	Web Exercises, NBIF Project Goals and Project Assignments	http://www.ncbi.nlm.nih.gov/ http://pedant.mips.biochem.mpg.de/frishman/pedant.html http://www.tigr.org/ http://www.nbif.org/	See Handout for citations to all published Genome Sequence Papers
3	CL	Jan 28	File management, operating systems, advanced web techniques, email	http://mode.lanl.k12.nm.us/tutorials/UNIX.html
4	PL	Feb 4	Whole Genome DNA Sequencing Strategies & Overview of Automated Technologies	http:biohome.htm LI-COR Random Sequencing Paper http://www.tigr.org/tdb/mdb/hidb/hidb.html	Read: Fleischmann et. al., Science 269:496-512 (1995) Copy @ Library or check out copy at Lammers office Room 371 Chem&Biochem and Read
5	CL	Feb 11	DNA Sequence assembly algorithms and packages, SEQUENCHER, TIGR ASSEMBLER	http://www.tigr.org/ http://www.genecodes.com	Sutton G.,White, O., Adams, M., and Kerlavage, A. (1995) TIGRsembler: A new tool for assembling large shotgun Sequencing projects. Genome Science & Technology 1:9-19).
6	CL/PL	Feb 18	DNA Sequence assembly algorithms and packages, SEQUENCHER, TIGR ASSEMBLER, and GENE INSPECTOR	Viewing Chromatographic Data in Sequencher
7	CL	Feb 25	String handling and searching using scripting and PERL language	http://www.perl.org/ http://www.metronet.com/perlinfo/perl5.html
		Mar 4	SPRING BREAK
8	CL	Mar 11	Mid- Term Exam PERL Language	http://language.perl.com/
9	CL	Mar 18	Advanced Search Algorithms	Gene Inspector Project Week 1 Instructions
10	PL	Mar 25	Basic sequence alignment and analysis techniques using different approaches	http://www.gcg.com/
11	PL	Apr 1	Basic BLAST Protein Domain Similarities	http://www.psc.edu/biomed/TUTORIALS/SEQUENCE/ DBSEARCH/tutorial.html
12	PL	Apr 8	Domain Hunting & Hidden Markov Modeling	http://www.sanger.ac.uk/Software/Wise2/hmmcrib.shtml http://genome.wustl.edu/eddy/hmmer.html#hmmer http://genome.wustl.edu/eddy/HMMER/manpage.html Gene Inspector Project Final Report Guidelines	Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjolander, and David Haussler. Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol., 235:1501--1531, 1994.
13	PL & CL	Apr 15	Homology Modeling	http://bonsai.lif.icnet.uk/people/rob/CCP11BBS/flowchart2.html http://expasy.hcuge.ch/swissmod/SWISS-MODEL.html http://www.embl-heidelberg.de/Services/sander/predictprotein/
14	PL & CL	Apr 22	Perl Project Work Day
15	Dr. John Spalding, PSL	Apr 29	"Computation Issues in Managing a Bioinformatics Project"	http://nbifb.psl.nmsu.edu/projects/protproj/protproj.html
16	PL & CL	May 6	Comparative Genomics EST Data: Libraries, Expresion Patterns and Information Processing
17		May 11 3:30	FINAL EXAM