Fall Semester, 2006 Sequence
Analysis Laboratory
(Biochem 712)
Tuesday
afternoons,
SYLLABUS
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* Denotes potential
credit-bearing activities |
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Sept 05 |
L01 |
Desktop Molecular
Graphics I: RasMol |
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Introduction
to pdb coordinate files, 3D graphics and graphic
scripts for molecular structure display using desktop computers. Programs
will include: RasMol. |
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Before
Class: |
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- Read
L01 sections of lab book |
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In Class: |
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- Show
up (1240 |
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- Complete
L01 lab book exercises, parts I and II |
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Homework: |
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- Begin
L01 homework sheet (given in class or online) |
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- Read
MG and L02 section of lab book |
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- Logon
to course web site, become familiar with resources |
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Sept 12 |
L02 |
Desktop Molecular
Graphics II: VMD & DeepView |
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Advanced
molecular graphics, scripting and publication quality 3D molecular surface
representations using desktop computers.
Programs will include: VMD & DeepView. |
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In Class: |
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- Complete
L02 lab book exercises |
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Homework: |
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- Read
L03 section of lab book |
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- Think
about partner selection for "My Molecule" L07 exercise |
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Sept 19 |
L03 |
Movies & Animations |
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Introduction
to creation of simple QuickTime, MPG and animated GIF movies from PowerPoint,
Rasmol and VMD. Programs will include: MS
PowerPoint, QuickTime, VMD, Rasmol |
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In Class: |
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-* Turn
in L01 homework |
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- Complete
L03 lab book exercises |
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- Select
partner(s) for “My Molecule” presentation project |
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Homework: |
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- Read
L04 section of lab book |
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- Begin
“My Molecule” project with partner(s) |
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Sept 26 |
L04 |
Desktop Molecular
Graphics III: PyMol |
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Advanced
molecular graphics with PyMol. GUI interface, movie
making and script writing. |
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In Class: |
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- Complete L04 lab book exercises |
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Homework: |
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- Read
L05 section of lab book |
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- Continue
“My Molecule” project (L07) with partner(s) |
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Oct 3 |
L05 |
Basic UNIX for GCG Users
I: Line Command Interface |
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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) Terminal, X11; (unix) pwd, ls, more, mkdir, man, ftp, history, cat, grep,
pico; (GCG) GenHelp, GenManual, PlotTest, ShowPlot, Reformat, Fetch. |
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In Class: |
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- Complete
L05 lab book exercises |
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Homework: |
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- Read
L06 section of lab book |
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- *Complete
L05 homework page (given in class or online) |
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- Complete
online practice quiz “unix-quiz” |
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- Continue
“My Molecule” project with partner(s) |
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Oct 10 |
L06 |
Protein Sequence Analysis |
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GCG (unix) overview of programs for protein sequence analysis and protein secondary structure prediction. Programs will include: (GCG) PeptideMap, Motifs, Isoelectric, HTHScan, CoilScan, SPScan. (DNASTAR) Protean. |
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In Class: |
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-*Turn
in L05 homework |
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Complete L06 lab book exercises |
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Homework: |
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-*Complete
L06 homework page (given in class or online, due Oct 24) |
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- Complete
“My Molecule” project with partner(s) |
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Oct 17 |
L07 |
Student Molecular
Graphics Presentations |
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Assigned
student presentations illustrating techniques in PowerPoint and molecular
graphics. Programs will include: (various). |
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In Class |
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- * Present
with partner(s) “My Molecule” graphic project |
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- Provide
feedback on presentations by other class groups |
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Homework: |
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- Read
L08 section of lab book |
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Oct 24 |
L08 |
Sequence Mapping and
Pairwise Comparison |
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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. |
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In Class: |
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- * Turn
in L06 homework sheet |
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- Complete
L08 lab book exercises |
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Homework: |
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-Read L09 section of lab book |
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Oct 31 |
L09 |
Multiple Sequence
Analysis |
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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. |
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In Class: |
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- Complete
L09 lab book exercises |
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Homework: |
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- Read
L10 section of lab book |
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- *Complete
L09 homework sheets (given in class or online) |
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Nov 07 |
L10 |
Database Searching |
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Internet- and
desktop-based overview of sequence databases, database searching, sequence
retrieval tools, Programs will include: (Macintosh) web browser, (online)
BLAST, FastA, ProSite, |
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In Class: |
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- Complete L10 lab
book exercises |
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Homework: |
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- *Complete
L10 homework sheets (given in class or online) |
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- Read
L11 section of lab book |
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Nov 14 |
L11 |
Desktop Molecular
Evolution |
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Internet- and
desktop-based overview of sequence alignments and phylogenetic
reconstruction. Programs will include: (Macintosh)
web browser, ClustalX, Paup.
(online) BLAST |
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In Class: |
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- * Turn
in L10 homework sheet |
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- *In class quiz on 712 materials to
date |
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- Complete
L11 lab book exercises |
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Homework: |
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- Read
L12 section of lab book |
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Nov 21 |
L12 |
Fragment Assembly and Lab
Datasets |
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Overview
of program (DNASTAR) for sequence gel assembly into contiguous
fragments. Practice datasets will help
assimilation of sequence analysis concepts to date. Programs will include:
(Macintosh) DNASTAR SeqMan. |
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In Class: |
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- * Complete
and turn in model reading exercise |
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- Complete
L12 lab book exercises |
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Homework: |
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- Read
L13 section of lab book |
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- Begin
L12 dataset problems |
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Nov 28 |
L13 |
Primers |
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Introduction
to DNASTAR desktop sequence analysis package PrimerSelect. Programs will include: (MacIntosh)
SeqMan, PrimerSelect,
(web) Primer3. |
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In Class: |
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-
Complete L13 lab book exercises |
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Homework: |
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- Read
L14 section of lab book (to be handed out in lab) |
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Dec 05 |
L14 |
Chromosomes: Sequences
and Databases |
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Advanced
exercise with on-line databases and large chromosome-size sequences. To be handed out and completed in class. |
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In Class: |
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- *Turn
in L12 dataset assignments |
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- Complete
L14 exercises |
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Homework: |
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- Read
L15 section of lab book (to be handed out in lab) |
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Dec 12 |
L15 |
RNA Folding |
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Overview
of programs to
predict and display optimal and suboptimal minimum-free energy secondary
structures of single-stranded RNAs. Programs will include: (unix- and web-based) Mfold. |
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In Class:
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- Complete
L15 lab book exercises |
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Finally: |
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- Pick up grades and datasets from ACP
(527B Bock Labs) on
Tuesday, December 19 |