Pabio 536 Lab session and Homework Week 8 Multiple Alignment 1. Perform a multiple alignment using the ACBP liver forms and the ACBP brain forms from this week’s sequence file and show the alignment (ALN file) you obtained (10 points). 2. Compare the pattern of identical residue s conserved within the liver forms to those conserved within the brain forms. Are there brain or li ver specific residues (ie residues conserved in liv er but not in brain or vice versa)? Provide a couple of examples (ie brain: A26, liver: W32)(10 points). 3. A) Determine a pattern of liver-specific amino acid residues, ie those amino acids conserved in all liver forms but not in the brain forms. Provide your pattern. (10 points) B) Do a PHI-BLAST search using the hum an ACBP Liver form in the query and your Liver-specific pattern “ limit your output to salmonids. Did you detect a putative liver ACBP form in the salmonid atlantic salmon salmo ? provide the BLAST hit. If you obtain no putative salm on ACBP hits try altering your pattern slightly and redo the PHI-BLAST. If a ll else fails, do a normal BLAST search with no pattern and exam the hits to see if you can detect a putative liver ACBP form in the salmonid atlantic salmon salmo? Provide the BLAST hit. In this last case, how did the salmo sequence differ from your patt ern (10 points) C) Do a multiple alignment of all of the liver forms in question 2 plus your putative salmon liver ACBP form “ pr ovide the alignment (10 points). D) Discuss the alignment with regard to other liver-specific re sidues that you did not include in your PHI-BLAST pattern, ie are those conserve d as well? Would you consider this putative atlantic salmon ACBP to be a liver form? Discuss (10 points). 4. A) Determine a pattern of amino acid re sidues that are conserved in the ACBP brain forms but not in the liver forms. Provide the pattern (10 points) B) Do a PHI-BLAST search using the huma n ACBP Brain form in the query and your Brain-specific pattern “ limit your output to salmonids. Did you detect a putative brain ACBP form in the Atlan tic salmon (Salmo salar)? If you obtain no putative salmon ACBP hits try altering your pattern slightly and redo the PHI-BLAST. If you still get no putativ e salmon ACBP hit try doing a protein BLAST without the pattern and look at the hits by eye to determine whether there is a brain form in Salmo salar (h int- you should detect one) (10 points) C) Do a multiple alignment of all of th e brain forms in question 2 plus your putative salmon brain ACBP form “ pr ovide the alignment. (10 points) D) Discuss the alignment with regard to the brain-specific residues? Would you consider this salmon ACBP to be a brai n form? Discuss in relationship to your PHI-BLAST pattern and other brain formspecific characteristics. (10 points) 5. EXTRA CREDIT: Do an alignment of a ll of the liver and brain form ACBP sequences including the salmon sequences . Identify the identical residues conserved within all the sequences and discuss with regard to cons ervation of the previously characterized ACBP motif s (10 points). Can you make any conclusion regarding how the brain and th e liver forms differ from each other “ relying upon what you know of the structur e of ACBP? (no right answer here “ something to think about). (10 points) For a custom paper on the above topic, place your order now! What We Offer: ¢ On-time delivery guarantee ¢ PhD-level writers ¢ Automatic plagiarism check ¢ 100% money-back guarantee ¢ 100% Privacy and Confidentiality ¢ High Quality custom-written papers
