Describe what practical steps you could do

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Reference no: EM133256680

Goal: Examine a putative homolog found using PSI-BLAST.
Given: Query sequence P14629.
Target: Sequence Q9UQ84.2
Iteration #1: PSI-BLAST Swiss-Prot database, limited to mammals (taxid:40674).
Iteration #2: Include any sequence with an E value of 1e-04 or lower.

Question 1 What did you set for the threshold and why?

Question 2 What type of nuclease (exo- or endo-) is Q9UQ84.2?

Question 3 Based on the Iteration 2 E value, can you definitively state that Q9UQ84 and P14629 are homologs? Why or why not?

Question 4 Confirm homology between Q9UQ84 and P14629 using pairwise BLAST alignment. Are they homologues based on the pairwise alignment E value?

Question 5 Why might BLAST have not found all homologs on the first iteration?

Question 6 Other than pairwise alignment, describe what else you could have done on your computer with BLAST and alignment tools to try to confirm homology between Q9UQ84.2 and P14629.

Question 7 Describe what practical steps you could do in the wet lab to try to confirm homology between Q9QUQ84.2 and P14629.

Reference no: EM133256680

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