Fundamentals of Sequence Analysis, 1998-1999 Problem set 8: Formatting data for publication. If you get stuck, refer to the OpenVMS and GCG resources in the class home page. References: See the GCG and EGCG documentation. Problem group 1. Plasmid Maps 1A. Produce a map of pBR322 (GB_SY:Synpbr322) showing all restriction sites that are present only once and all major features. Problem group 2. Multiple sequence formatting Align all Troponin C entries in SwissProtein. 2A. Format the .MSF file using Pretty showing the consensus and differences. 2B. Format the .MSF file using PrettyPlot. Make the consensus Black, identity Green, similarity Blue, and differences Red. Also, turn off the boxes around similar sequence. 2C. Format the .MSF file using PrettyBOX. Show a consensus, using output lines of 50 characters with no "block" spacing on the line. Otherwise, use the default settings. Problem group 3. Single sequence formatting 3A. Format GB_IN:Dmhish1 for publication showing: 1. Protein translation under the DNA (3 letter form) 2. Forward sequence only (no reverse sequence) 3. Dots every 10 bases, above the DNA 4. Number at the ends of the dot line 5. Two blank lines between each group of lines 50 bases per line Problem group 4. Moving graphics files to your own machine 4A. Configure GCG graphics to use the CGM, EPSF, or HPGL graphics driver, then regenerate the PlasmidMap graphic from problem 1, being careful to use the /FONT=0 qualifier, and move the file so produced to your Macintosh or Windows machine. Which programs do you have, if any, which could open/import the file? Which pieces were you able to modify?