Fall Semester, 2004 Sequence Analysis Laboratory (Biochem 712)

Tuesday afternoons, 1:20-3:30 pm, BNMC Computer Lab, 1240 Biotech Center, 1 cr.

SYLLABUS

* Denotes potential credit-bearing activities
Sept 07	L01	Desktop Molecular Graphics I: RasMol
	Introduction to pdb coordinate files, 3D graphics and graphic scripts for molecular structure display using desktop computers. Programs will include: (Macintosh) RasMol.
	Before Class:
		- Read L01 sections of labbook
	In Class:
		- Show up (1240 Biotech Center computer lab) ready to go!
		- Complete L01 labbook exercises, parts I and II
	Homework:
		- Begin L01 homework sheet (from labbook or online)
		- Read MG and L02 section of labbook
		- Logon to course web site, become familiar with resources
Sept 14	L02	Desktop Molecular Graphics II: VMD & DeepView
	Advanced molecular graphics, scripting and publication quality 3D molecular surface representations using desktop computers. Programs will include: (Macintosh) VMD & DeepView.
	In Class:
		- Complete L02 labbook exercises
	Homework:
		- Read L03 section of labbook
		- Think about partner selection for My Molecule L06 exercise
Sept 21	L03	Movies & Animations
	Introduction to creation of simple QuickTime, MPG and animated GIF movies from PowerPoint, Rasmol and VMD. Programs will include: (Macintosh) MS PowerPoint, QuickTime, VMD, Rasmol, Gimp
	In Class:
		-* Turn in L01 homework renderings (if not submitted electronically)
		- Complete L03 labbook exercises
		- Select partner(s) for “My Molecule” presentation project
	Homework:
		- Read L04 section of labbook
		- Begin “My Molecule” project (L06) with partner(s)
Sept 28	L04	Basic UNIX for GCG Users I: Line Command Interface
	Introduction to Internet communications software, the unix operating system, Wisconsin Sequence Analysis Package (GCG) command line entry, graphics initialization and file transfer procedures. Programs will include: (Macintosh) Fetch, Terminal; (unix) pwd, ls, more, mkdir, man, ftp, history, cat, grep, pico; (GCG) GenHelp, GenManual, PlotTest, ShowPlot, Reformat, Seqed, Fetch, Composition, Translate, Frames
	In Class:
		- Complete L04 labbook exercises
	Homework:
		- Read L05 section of labbook
		- *Complete L04 homework page (from book or online)
		- Complete online practice quiz “unix-quiz”
		- Continue “My Molecule” project with partner(s)
Oct 05	L05	Protein Sequence Analysis
	GCG (unix) overview of programs for protein sequence analysis and protein secondary structure prediction. Programs will include: (GCG) PeptideMap, Motifs, PeptideStructure, PlotStructure, PepPlot, Isoelectric, HTHScan, CoilScan, SPScan.
	In Class:
		- Complete L05 labbook exercises
		-*Turn in L04 homework
	Homework:
		- *Complete L05 homework page (from book or online, due Oct 19)
		- Complete “My Molecule” project with partner(s)
Oct 12	L06	Student Molecular Graphics Presentations
	Assigned student presentations illustrating techniques in PowerPoint and molecular graphics. Programs will include: (various).
	In Class:
		- * Present with partner(s) “My Molecule” graphic project
		- Provide feedback on presentations by other class groups
	Homework:
		- Read L07 section of labbook
Oct 19	L07	Sequence Mapping and Pairwise Comparison
	Overview of GCG (unix) programs and associated data tables for restriction mapping and pairwise sequence comparison. Programs will include: (GCG) Map, MapSort, MapPlot, PlasmidMap, Compare, DotPlot, BestFit, Gap.
	In Class:
		- * Turn in L05 homework sheet
		- Complete L07 labbook exercises
	Homework:
		- Read L08 section of labbook
Oct 26	L08	Multiple Sequence Analysis
	GCG (unix) overview of programs for creating, editing and evaluating multiple sequence alignments. Programs will include: (GCG) PileUp, PlotSimilarity, Lineup, Pretty, ProfileMake, ProfileSearch, ProfileSegments, ProfileScan. (Optional, GCG) Distances, OldDistances, Growtree, PaupSearch, PaupDisplay.
	In Class:
		- Complete L08 labbook exercises
		- Optional: complete section L00
	Homework:
		- Read L09 section of labbook
		-*Complete L08 homework sheets (from labbook or online)
Nov 02	L09	Database Searching
	Internet- and desktop-based overview of sequence databases, database searching, sequence retrieval tools, Programs will include: (Macintosh) Netscape, (online) BLAST, FastA, ProSite,
	In Class:
		- *In class quiz on 712 materials to date.
		- Complete L09 lab book exercises
	Homework:
		-*Complete L09 homework sheets (from labbook or online)
		- Read L10 section of labbook
Nov 09	L10	Desktop Molecular Evolution
	Internet- and desktop-based overview of sequence alignments and phylogenetic reconstruction. Programs will include: (Macintosh) Netscape, (online) BLAST, ClustalW, Paup.
	In Class
		-* Turn in L09 homework sheet
		- Complete L10 labbook exercises
	Homework:
		- Read L11 section of labbook
Nov 16	L11	Fragment Assembly and Lab Datasets
	Overview of programs (GCG and DNASTAR) for sequence gel assembly into contiguous fragments. Practice datasets will help assimilation of sequence analysis concepts to date. Programs will include: (GCG) GelStart, GelEnter, GelMerge, GelAssemble, GelView, (Macintosh) DNASTAR Megalign.
	In Class:
		-* Complete and turn in model reading exercise
		- Complete L11 labbook exercises
	Homework:
		- Read L12 section of labbook
Nov 23	L12	Dataset Project
	In-class project on fragment assembly and sequence analysis tools.
	In Class:
		- Begin datasets assignments (due on Dec 7)
	Homework:
		- Read L13 section of labbook
Nov 30	L13	Primers
	Introduction to DNASTAR desktop sequence analysis package PrimerSelect. Programs will include: (MacIntosh) SeqMan, PrimerSelect, (GCG) Primer.
	In Class
		- Complete L13 labbook exercises
	Homework:
		- Read L14 section of labbook (to be handed out in class)
Dec 07	L14	Chromosomes: Sequences and Databases
	Advanced exercise with on-line databases. To be handed out and completed in class
	In Class:
		-*Turn in L12 dataset assignments
		- Complete L14 exercises
	Homework:
		- Read L15 section of labbook
Dec 14	L15	RNA Folding
	Overview of GCG (unix) and web-based programs to predict and display optimal and suboptimal minimum-free energy secondary structures of single-stranded RNAs. Programs will include: (GCG) StemLoop, Mfold, Squiggles, Mountains, Circles, DotPlot; (web-based) Mfold.
	In Class:
		- Complete L14 labbook exercises
	Finally:
		- Pick up grades and datasets from ACP (527B BockLabs) on Tuesday, December 21

A.C. Palmenberg, instructor of record: Dept of Biochemistry (2-7519; acpalmen@wisc.edu, 527B Bock Laboratories)

J.-Y. Sgro: Biotechnology Center (2-7464; jsgro@wisc.edu, 731-B BockLabs)

M. Hill: Dept of Biochemistry (2-7228; mhill@biochem.wisc.edu, 511 BockLabs)