BIOL_A108 Module 2 Bioinformatics Exercise:
Sequence Alignment and Phylogenetics
25 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 penalty
PM = theoretical sum of all matches (no mismatches)
Alignment Score, S = S(PM) – Penalties

QUE1: TTCGATTACCTCAAGTCGA S(PM) = _______?
SUB1: TTCGATTACCTCAAGTCGA

QUE1: 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 bear
ATGGTACCAT

5’3’ Sequence 4: Black Bear
ATAGTACTGT

5’3’ Sequence 5: Polar Bear
TTGGTACCAT

5’3’ Sequence 6: Cave Bear
ATGGCGCCAT

(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=9606
Cave bears!
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6590514/