Fundamentals of Sequence Analysis, 1995-1996 Problem set 5: Assembling sequences. If you get stuck, refer to the OpenVMS and GCG resources in the class home page. References: See the GCG and EGCG manuals. Problem group 1. Dealing with ABI sequences Create a subdirectory and set your default directory to it. Issue the command: $ copy class:*example*.*  You will now see two files with ugly names. 1A. How do you fix these names? Configure your terminal for GCG graphics. Issue these commands: $ abiprintout/infile=ABI_EXAMPLE_M13F.ABI;1/begin=180/end=200 $ abiprintout/infile=ABI_EXAMPLE_M13F.ABI;1/begin=180/end=200/pnt=500 1B. How do the two plots differ? 1C. What two commands could be used to get the sequence into GCG format? What two commands could you use to extract a subsequence (ie, trim off the cruddy sequence on the ends)? Problem group 2. Sequence assembly (When you are done remember to delete the files created during this exercise!) Create a sequencing project (assuming that bluescript was the only vector used) and use gelenter to put into it these files: class:test*.seq class:bad*.seq class:rest*.seq Assemble it. 2A. What was wrong with bad0002.seq? What was wrong with bad0001.seq? 2B. Is there a difference in the quality of the TEST* and REST* sequences? 2C. Ignoring the BAD0001 contig, there are two contigs covering 1164 and 1569 bases (the pieces were shotgunned from a fragment of size 3000). Should you continue with shotgun sequencing for this insert? 2D. Anything else you might want to do?