M01 Creating Powerpoint Presentations
Instructional BioModule to introduce faculty, staff and students to basic elements of MS Powerpoint presentation graphics for their classes and seminars. Programs include: (Macintosh) MS Powerpoint.
M02 Desktop Molecular Graphics: Chime, WebLabViewer, Movies, Animations, Publication Quality Graphics
BioModule unit to accompany M03. Exercises cover essential commands in Chime and WebLabViewer graphics packages for creation of publication quality molecular displays. The design and use of Rasmol scripts for creating QuickTime or Animagic movies is also explored. , Programs include: (Macintosh) Rasmol, Chime, Sparkle, WebLabViewer Lite.a
M03 Desktop 3D Molecular Graphics: RasMol
BioModule to introduce faculty, staff and students to pdb coordinate files and 3D graphics for molecular structure display, using desktop computers. Simple script files for animation of structures will be illustrated and created. Programs include: (Macintosh, multiplatform) RasMol.
M04 Basic Unix for GCG Users
Introduction to internet communication software, the unix operating system, Wisconsin Sequence Analysis Package (GCG) command line entry, graphics initialization and file transfer procedures. Designed for faculty, staff and students who intend to take any other M05-M11 BioModule unit. Programs include: (Macintosh) Fetch, telnet; (unix) pwd, ls, more, mkdir, man, ftp, history, cat, grep, vi; (GCG) GenHelp, GenManual, PlotTest, ShowPlot.
M05 Using Sequences and Databases
Overview of key GCG (unix) programs and file formats for sequence editing, translation, reading frame and database lookup functions. Prerequisites: M04 BioModule or equivalent. Programs include: (GCG) Reformat, SeqEd, Reverse, Publish, Composition, Frames, Translate, Lookup, StringSearch, Fetch.
M06 Protein Sequence Analysis
GCG (unix) overview of programs for protein sequence analysis and protein secondary structure prediction. Prerequisites: M04 BioModule or equivalent. Programs include: (GCG) PeptideMap, Motifs, PeptideStructure, PlotStructure, PepPlot, Isoelectric, HTHScan, CoilScan, SPScan.
M07 Sequence Mapping and Comparison
Overview of GCG (unix) programs and associated datatables for restriction mapping and pairwise sequence comparison. Prerequisites: M04 BioModule or equivalent. Programs include: (GCG) Map, MapSort, MapPlot, PlasmidMap, Compare, DotPlot, BestFit, Gap.
M08 Web-based Sequence Database Searching
Internet-based overview of sequence databases, including Prosite, database searching and sequence retrieval tools. Prerequisites: none. Programs include: FastA, Blast .
M09 Multiple Sequence Analysis
GCG (unix) overview of programs for creating, editing and evaluating multiple sequence alignments. Prerequisites: M04 and M07 BioModules or equivalent. Programs include: (GCG) PileUp, PlotSimilarity, Pretty, Consensus, ProfileMake, ProfileSearch, ProfileSegments, Distances, Pretty.
M10 Molecular Evolution
Overview of GCG (unix) and desktop programs for evaluating the potential evolutionary relationships of sequences within a multiple alignment. Prerequisites: M04 BioModule or equivalent. Programs include: (GCG) Pileup, Distances, PaupSearch, PaupDisplay.
M11 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. Prerequisites: M04 BioModule or equivalent. Programs include: (GCG) StemLoop Mfold, Squiggles, Mountains, Circles, Compare, DotPlot; (web-based) Mfold.
Overview of GCG's graphical interface. SeqLab provides graphical access to the ~50 most used GCG programs. FREE X-windows emulation is available for both Mac/Windows desktop computers. Prerequisites: none. Programs will include: (GCG) SeqLab and the reprise of GCG programs used with the line command interface, e.g. Gap, Pileup, PlotSimilarity, etc.
Introduction to the DNASTAR Lasergene program suite. Highlights will focus on "Gene Discovery", a new integrated software for sequence analysis, annotation and publication. Other DNASTAR software tutorials include "PrimerSelect" and "SeqMan II" for sequence assembly and contig management. Prerequisites: none.