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. References: 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 Controls 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 exon.) 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?