Practical Applications of Sequence Analysis Course Information DATES: Tuesday April 3, 2001 - Tuesday June 5, 2001 TIMES: Tuesdays: 3:00 - 4:30 Thursdays: 1:00 - 2:30 LOCATION: Bevill Biomedical Research Building Lecture Hall (BBRB 170) 845 19th Street South INSTRUCTOR: Elliot Lefkowitz, Ph.D., Department of Microbiology Office: 277A BBRB Phone: 4-1946 (Voice); 5-5240 (FAX) E-mail: [email protected] WEB SITE: http://genome.microbio.uab.edu/MIC753/ GCG DOCS: http://genome.microbio.uab.edu/GCG/GCG10/gcgmanual.html (See Elliot for the username and password for access) REQUIRED Hardware and Software • A computer with access to the Internet • Communication Software o A World-Wide-Web Browser such as Netscape (v 4.6+) or Internet Explorer (v5.0+) o A VT100 and graphics terminal emulator program o An XWindows emulator program • Macintosh o VT100/Graphics: NCSA Telnet (freeware) o VT100/Graphics: VersaTerm Pro (Synergy Software $195) o XWindows: eXodus (Powerla n Software $149) • Windows PC o VT100/Graphics: TeraTerm Pro (freeware) o VT100/Graphics: SmarTerm Office (Esker Software) o XWindows: X-Win32 (Starnet Communications Corporation $149; $60 Student license) o XWindows: WebTerm X (Powerlan Software $149) The GCG Server: analyze This is the UNIX Computer of the Molecular and Genetic Bioinformatics Facility at UAB that runs the Genetics Computer Group (GCG) software and maintains the sequence databases. • SYSTEM MANAGER: Elliot Lefkowitz • INTERNET ADDRESS: gcg.genome.uab.edu (or analyze.genome.uab.edu)Computer Access All registered students will be provided with computer accounts on analyze. These accounts will be active until completion of the course requirements, and are provided without charge. Those not registered can obtain computer accounts by following instructions on the following web page: http://genome.microbio.uab.edu/GCG/GCGatUAB.htm (See Elliot for a username and password to access this page.) Reference Material General Sequence Analysis and Bioinformatics GCG Documentation Version 10.1 (UNIX) User’s Guide Program Manual A Practical Guide to the Analysis of Genes and Proteins (Strongly Recommended) Andreas Baxevanis(Editor), B.F.Francis Ouellette(Editor). John Wiley & Sons, 1998 Sequence, Structure, and Databanks : A Practical Approach Des Higgins (Editor), Willie Taylor (Editor). Oxford Univ Press, 2000 Sequence Analysis Primer Michael Gribskov and John Devereux (eds.) Groves Press, 1991 Sequence Analysis in Molecular Biology Gunnar von Heijne Academic Press, 1987 Genomics Cracking the Genome : Inside the Race to Unlock Human DNA Kevin Davies Free Press, 2001 Genome Matt Ridley Harpercollins, 2000Phylogenetic Analysis Molecular Systematics David M. Hillis and Craig Moritz (eds.) Sinauer Associates, 1990 MacClade; Analysis of Phylogeny and Character Evolution Wayne P. Maddison and David R. Maddison Program and Manual (Macintosh) Sinauer Associates, 1992 PAUP*; Phylogenetic Analysis Using Parsimony David L. Swofford Program and Manual, version 4.0 (Macintosh; UNIX; DOS) Sinauer Associates Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences Methods in Enzymology, Vol. 183, Doolittle, R.F. (ed.) Academic Press,