Sequence Alignment and Phylogenetics | homework crew
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BIOL_A108 Module 2 Bioinformatics Exercise:Sequence Alignment and Phylogenetics25 pts. Individual, due week 7 W/Th. in lab. You can collaborate with your group.Name: Section/TA:1. (5pts.) DNA sequence alignment. Quantify DNA sequence alignment scores for QUE1/SUB1, QUE1/SUB4, and QUE1i/SUB5. The three alignments are below. The scoring system is:match = +1; mismatch = 0 (-1 penalty); gap = -1 penaltyPM = theoretical sum of all matches (no mismatches)Alignment Score, S = S(PM) – PenaltiesQUE1: TTCGATTACCTCAAGTCGA S(PM) = _______?SUB1: TTCGATTACCTCAAGTCGAQUE1: TTCGATTACCTCAAGTCGA S = ___________?SUB4: TTCG-TAGC—AAGTCCA (show your math)QUE1i: TTCGATTACCTCAAGT-CGA S = ___________?SUB5: TTCG-TTAC-TTAC-TTCG- (show your math)2. (20pts.) Phylogenetics. You have short DNA sequences from four species of bears.(a) Analyze and score all pairwise sequence alignments using the scoring system above. Calculate S for Brown:Brown (theoretical perfect match), Brown:Black, Brown:Polar, Brown:Cave; Black:Polar, Black:Cave; Polar:Cave.5’3’ Sequence 3: Brown bearATGGTACCAT5’3’ Sequence 4: Black BearATAGTACTGT5’3’ Sequence 5: Polar BearTTGGTACCAT5’3’ Sequence 6: Cave BearATGGCGCCAT(b) Draw a simple neighbor-joining phylogenetic tree, using the S alignment scores you calculated above, to map bear species closest relatives and evolution. Justify (explain) why you think your tree reflects bear evolutionary relationships.Deep thinking question: Identify one limitation of this method. How might you estimate your confidence that the DNA-sequence based phylogenetic tree accurately reflects evolutionary relationships among the 4 bear species?Resources:Open Access to the Human Genome pages (NCBI):https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=info&id=9606Cave bears!https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6590514/
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