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712 GENERAL INFORMATION

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Fall Semester, 2002 Sequence Analysis Laboratory (Biochem 712)

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

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, 721 BockLabs)

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

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SYLLABUS

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* Denotes potential credit-bearing activities

Sept 03 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 10 L02 Desktop Molecular Graphics II: WebLabViewer & Chime

Advanced molecular graphics, scripting and publication quality 3D molecular surface representations using desktop computers. Programs will include: (Macintosh) WebLabViewer, Netscape, Chime.

In Class:

- Complete L02 labbook exercises

Homework:

- Read L03 section of labbook

- Think about partner selection for My Molecule L06 exercise

Sept 17 L03 PowerPoint and Animated Movies

Introduction to basic elements of Microsoft PowerPoint and the creation of simple QuickTime movies and PICT file graphics for PowerPoint presentations. Programs will include: (Macintosh) MS PowerPoint, QuickTime, Sparkle.

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 24 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, MacSSH; (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 01 L05 Basic UNIX for GCG Users II: X-Win Graphical Interface

Introduction to GCG via SeqLab interface using X-windows and Internet browsers

Overview of key GCG (unix) programs and file formats using SeqLab. Programs will include: (GCG) SeqLab, Reformat, Translate.

In Class:

- *Turn in L04 homework sheet

- * In-class quiz (materials from L01, L02 and L04)

- Complete L05 labbook exercises

Homework:

- Complete “My Molecule” project with partner(s)

Oct 08 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 15 L07 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 L07 labbook exercises

Homework:

- Read L08 section of labbook

- Complete L07 homework sheet (from labbook or online)

Oct 22 L08 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 L07 homework sheet

- Complete L08 labbook exercises

Homework:

- Read L09 section of labbook

Oct 29 L09 Multiple Sequence Analysis

GCG (unix) overview of programs for creating, editing and evaluating multiple sequence alignments. Programs will include: (GCG) PileUp, PlotSimilarity, Lineup, Pretty.

In Class:

- Complete L09 labbook exercises

Homework:

- Read L10 section of labbook

- Complete L09 homework sheets (from labbook or online)

Nov 05 L10 Profiles and Molecular Evolution

Overview of GCG (unix) and desktop programs for evaluating the potential evolutionary relationships of sequences within a multiple alignment. Programs will include: (GCG) ProfileMake, ProfileSearch, ProfileSegments, ProfileScan, Distances, OldDistances, Growtree, PaupSearch, PaupDisplay.

In Class:

- * Turn in L09 homework sheet

- *In class quiz on materials from L07, L08, and L09

- Complete L10 labbook exercises

Homework:

- Read L11 section of labbook

Nov 12 L11 Database Searching

Internet-based overview of sequence databases, database searching and sequence retrieval tools. Programs will include: (Macintosh) Netscape, BLAST, FastA, ProSite.

In Class:

- Complete L11 labbook exercises

Homework:

- Read L12 section of labbook (to be handed out in class)

- Complete L11 homework sheets (from labbook or online)

Nov 19 L12 Molecular Evolution Project

Advanced exercise on molecular evolution. To be handed out and completed in class.

In Class:

- Complete L12 exercises

Homework:

- Read L13 section of labbook

Nov 26 L13 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 L13 labbook exercises

- Receive and begin dataset assignments

Homework:

- Read L14 section of labbook

- Continue working on dataset assignments

Dec 03 L14 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

Homework:

- Read L15 section of labbook

- Complete dataset assignments

Dec 10 L15 Primers

Introduction to DNASTAR desktop sequence analysis package PrimerSelect. Programs will include: (MacIntosh) SeqMan, PrimerSelect, (GCG) Primer.

In Class

- *Turn in dataset assignments

- Complete L15 labbook exercises

Finally:

- Pick up grades and datasets from ACP (527B BockLabs)

on Tuesday, December 17