Title: BIO520 Bioinformatics Fall 2005
Author: Jim Lund
Company: College of Arts and Sciences

BIO520 Bioinformatics Fall 2005					 Name:
EXAM2

You may use any books, notes, web pages, software programs, or related materials to complete this exam.  You MAY NOT consult with any person regarding the exam’s intellectual content.
1.  Examine the Genscan gene predictions for a human genomic sequence.  
 a. (2 pts) For each predicted gene, give the number of exons and the strand.  

 b. (1pt)  Indicate which gene is least likely to be a correct prediction.
 
c. (2 pts) How useful is an EST that matches to a single, contiguous stretch of DNA sequence in gene prediction?  

2. (1 pt) Which is more strongly conserved, protein primary, secondary, or tertiary structure?  (Circle one)

3. (2 pts) You are studying the human Retinoic Acid Nuclear Receptor Hrar and want to compare its structure to that of the mouse ortholog to look for differences that could account for different experimental results with the human and mouse genes.  You know that structures have been determined for both proteins.  What software programs or web tools would you use to align and compare the two structures?

4. (3pts) When comparing orthologous protein sequences from two species is the number of aa changes directly proportional to the time the two species diverged?  Briefly explain why or why not.

5. Refer to the phylogenetic tree below.
a. (1 pt) What best describes the relationship between the human B1 and human B2 sequences: paralog, ortholog, homolog, or none of these terms?
 b. (1pt) Circle an otholog of rabbit B1 in the tree below. 

6. Examine the phylogenetic tree below.  Bootstrap scores using 1000 trials are indicated to the right of each node.
a. (1pt) Indicate the clade with the lowest reliable confidence score.
b. (1pt) Indicate a low confidence clade.

988

958

999

786

1000

503

926

496

530

7. (2 pts) In genome sequencing projects one approach is to cloned the genomic DNA into vectors of several different size ranges  (5kb, 20kb, 150kb) for further subcloning and sequencing.  What is the advantage of using vectors of different sizes?

8. (3 pts) How does the Ensembl gene prediction and annotation system differ from ab initio gene prediction?