Part A: Identifying SNPs
1) Per your teacher’s directions, open the digital document that has been assigned to you.
2) Take one minute to visually scan the two sequences to see if you can find a single-nucleotide polymorphism (SNP) in the variant allele.
MTB_Variant_A
MTB_Variant_B
MTB_Variant_C
MTB_Variant_D
MTB_Variant_E
MTB_Variant_F
MTB_Variant_G
MTB_Variant_H
3) Did you find it? _______ Describe the experience of comparing these two allele sequences. Is it easy? Difficult? Explain. What could make this process easier?
4) Comparing gene sequences by hand is a time-consuming process. Fortunately, computer programs have been created to make this task happen almost instantaneously.
a.Open your computer’s internet browser and go to ClustalW at http://www.genome.jp/tools/clustalw/.
b. On ClustalW, next to ‘Enter your sequences…’ click on DNA.
c. Copy and paste both of your gene sequences into the large empty box. Be sure to include the sequence labels (e.g. >wild-type_TB) for each sequence. The > symbol should start a new line.
d. Click ‘Execute Multiple Alignment.’
e. On the page that comes up, scroll down to the section headed with ‘clustalw.aln.’
f. Look at the alignment of your two sequences. Stars (***) indicate bases that are identical. An empty space indicates a SNP.
5) What is the base change? The base in the wild-type TB allele is a(n) _______ while the base in my variant allele is a(n) _______.
6) Based on what you have done in class so far, what would you have to do in order to determine if the amino acid sequence changes due to the SNP?
7) Look back at the top of your ClustalW alignment results. Locate how many base pairs (bp) are in this allele segment: ________ bp. Describe mathematically how you could calculate how many amino acids are coded for by this segment of the allele?
Perform that calculation. This segment of the rpoB allele codes for a polypeptide sequence that is _______ amino acids long.
Link to Part B
Copyright © 2013 Michael Strong and Jessica Taylor