BIO520 Exam 1 Spring 2008
Please email this lab to Yeshi (tgyeshi@uky.edu) with a subject line "BIO520 Exam 1" and name the document like so: "LundJ_exam1" or hand in written answers. Fill in your name on the exam!
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 exams intellectual content.
1. Find the NCBI mucleotide and protein RefSeq entries for chimpanzee KIFC3. Also find the RefSeq genomic clone containing this gene. Give the Accession numbers as your answer. There are two transcript variants and either is acceptable.
2.Examine the linked Genbank entry for human presenilin 1.
a. Is this a curated or automatically generated RefSeq entry?
b. How long is the 5' UTR for this gene?
c. What genes are adjacent to human presenilin 1 on the chromosome?
3. Examine the BLAST search results for human kinesin 18A linked here for this question: BLAST results (or here).
a. What database was searched?
b. Which scoring matrix was used in this BLAST search?
c. Examine the match to zebrafish protein NP_956533.1. What percent identity and percent positives are found in this alignment?
d. Give the E-value for this alignment and indicate whether it indicates a strong, moderate, or weak match.
e. Do the results for this search show all the matches to human kinesin 18A in this database? Give a yes or no answer and a brief explanation.
4. Match the scoring matrix with the situation in which its most appropriate to use:
| A. BLOSUM45 | 1. General search with no prior knowledge of relationship among potential results |
| B. BLOSUM62 | 2. Search for more distantly related members of a protein family. |
| C. BLOSUM80 | 3. Search for HSPs of high sequence similarity from closely related proteins |
5. In the PAM120 scoring matrix, what does the "120" refer to? Give a brief answer.
6. In the BLAST algorithm, alignments are seeded by word matches between the query sequence and database sequences. Do all word matches result in alignments shown in the BLAST results?
7. The Populus trichocarpa is currently being sequenced. You have an mRNA sequence for your gene and are eager to find the genomic sequence so you can analyze its promoter. You can not find this sequence in the nr database. Which BLAST program/database search will allow you to find the genomic DNA for your gene?
8 a. In the clustal results linked to here describe the first three alignment steps Clustal would make as it builds this multiple sequence alignment. Alignment produced using CLUSTAL defaults and the set of seqeunces in file clustal.fasta.
8 b. What steps would you take to refine and improve this multiple alignment?
9. Shown below is a ten amino acid PSSM. After the matrix are questions refering to it.
| Positon(columns))/AA(rows) | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
| A | -3 | 0 | -2 | -1 | 0 | -2 | -3 | -1 | -1 | -3 |
| G | -5 | -4 | -5 | -3 | 4 | -5 | 3 | 1 | 0 | -5 |
| I | 2 | 2 | -3 | -5 | 1 | -3 | -1 | 0 | -3 | 6 |
| L | -2 | -1 | -3 | -5 | -2 | -3 | 2 | -1 | -1 | 1 |
| V | 1 | 0 | -3 | -5 | -1 | -3 | -1 | -1 | -2 | 1 |
| M | 1 | -2 | -3 | -4 | -3 | -3 | -2 | 2 | -3 | -1 |
| F | 3 | 1 | -4 | -5 | -4 | -4 | -4 | -3 | -3 | 2 |
| W | -2 | -4 | -4 | -6 | -4 | -4 | -4 | -4 | -4 | -4 |
| P | 0 | 0 | -5 | -4 | -4 | -5 | -4 | -4 | 5 | -5 |
| C | -4 | 1 | 11 | -5 | 4 | 11 | -4 | -4 | -4 | -3 |
| S | 0 | 3 | -3 | -2 | -1 | -3 | 0 | 1 | -2 | -1 |
| T | -3 | 3 | -3 | -1 | 0 | -3 | -3 | 1 | 0 | -3 |
| Y | 6 | -3 | -4 | -4 | 0 | -4 | -4 | 0 | 1 | -2 |
| N | 0 | -3 | -5 | 4 | 1 | -5 | 1 | 1 | 1 | -1 |
| Q | -3 | -2 | -5 | -2 | -3 | -5 | 2 | 1 | -2 | -4 |
| H | -2 | -3 | -5 | 3 | 3 | -5 | -3 | 1 | 2 | 2 |
| K | -3 | 0 | -5 | 0 | -3 | -5 | 1 | 2 | -2 | -4 |
| R | 1 | 1 | -6 | -1 | -4 | -6 | 0 | -2 | -3 | -4 |
| D | -4 | -3 | -6 | 6 | -3 | -6 | -1 | -3 | 1 | -5 |
| E | -4 | -1 | -6 | -1 | 0 | -6 | -1 | 0 | 3 | -4 |
a. What is the most favored aa at the first position in the PSSM?
b. What is the least favored aa at the first position in the PSSM?
c. Give the consensus sequence corresponding to this PSSM.
d. Describe how the aa preferences differ at position 1 and position 6 (in addition to the obvious difference in most favored amino acids at the two postions).
