Sequence Alignment and Phylogenetics | homework crew



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/

Thanks for installing the Bottom of every post plugin by Corey Salzano. Contact me if you need custom WordPress plugins or website design.

Comments are closed.

Order

Hi there! Click one of our representatives below and we will get back to you as soon as possible.

Chat with us on WhatsApp
%d bloggers like this: