Bioinformatic Exam
Why and when should you prefer PSI-BLAST over blastp?
Why e-values differ in PSI-BLAST from first search to second iteration?
What does PSSM stand for? Which BLAST search program uses the PSSM?
In what situation one needs to verify two putative homologs using pairwise alignment and why?
Use PSI-BLAST to find homologues of protein P14629 (select uniprot/swissprot database),
limited to vertebrates.
What threshold did you use and why?
What type of enzyme shows up in almost every description?
Find the protein with accession number Q9UQ84.2. What is the enzyme?
What is the E value for Q9UQ84.2? Confirm homology between Q9UQ84.2 and P14629 using pairwise BLAST alignment.
What is the E value?Are they homologues based on that E value?
Why might BLAST have not found all homologs on the first iteration?
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.
Describe what else you could do in the wet lab to try to confirm homology between Q9QUQ84.2 and P14629.
