Fundamentals of Sequence Analysis, 1995-1996
Problem set 4:  Tools for Molecular Biology I.

If you get stuck, refer to the OpenVMS and GCG resources in the 
class home page.

 See documentation in the programs themselves.

Problem group 1.  Mapping

You have a cloned a new insert into your favorite vector.  Following single
and double digestions with enzymes Chmp and Bite you find the following 
mobilities (in cm. from the gel origin):

   Chmp cm 2.14    7.36    8.94
   Bite cm 3.62    5.36    6.90
   Chmp + Bite
        cm 5.36    6.90    7.36    8.30    8.94
        MW 2200    4300    5700    8600
        cm 8.25    5.48    4.32    2.62

1A.  What are the Molecular weights of the various pieces?

1B.  What is the restriction map?

Problem group 2.  Silent translation sites

You have cloned an mRNA for the NBLPRZ gene.  The sequence is in the file
"class:nblprz.seq".  You need to make a gene fusion construct taking as
much of the NBLPRZ gene as possible and attaching it to a stub protein.
The clone for that stub protein happens to have a HindIII site in convenient
place, the first base of which begins in the third base position of the 
codons in the open reading frame.  The NBLPRZ protein begins with the Met at
position 57.

2A.   If you engineer a translationally silent HindIII site into NBLPRZ,
      how much of it can you put into the fusion? 

2B.   How much better could we do if the convenient site on the stub 
      protein was for an XbaI (T'CTAG_A) the first base of which began
      on the first base of a codon in the open reading frame?

Problem group 3.  Primers

3A.  Design a set of primers to amplify at least bases 100 - 900 of
     CLASS:NBLPRZ.SEQ from genomic DNA (assume that it consists of a single

Problem group 4.  Finding genes

4A.  What are the predicted exons for the Drosophila gene in
     CLASS:UNKNOWN.SEQ?  (Use genefinder, the file is  already in the
     correct format for that program).  Identify the gene.  Do the
     predicted exons agree with the documented ones?