CSE 190: Assignment 3 Due Feb 25th, 2022 Late Due Date Mar 1st, 2022 for 50% credit (15 points) Complete the following questions and upload a PDF of your answers to Gradescope. Please be sure to describe your approach thoroughly and partial credit may be awarded even if the final answer is incorrect. Questions 1. Given the following spectrum of sequence mass 15 in a species with only two amino acids, mass(A) = 2 Da and mass (B) = 3 Da, calculate the number of possible sequences matching five peaks to the spectrum. Attach a printout of the completed spreadsheet. (4 points) 2. Using the following mappings between peptides and proteins, where each protein might be from a different species. a. Which, if any, proteins are matched by peptides that don’t match to any other protein (1 point) b. Which proteins are subset proteins (match to a subset of peptides of another protein) What is a potential explanation for a protein matching a subset of peptides also matched by another protein (2 points) c. Applying the maximum parsimony algorithm from slide 19 in the slide deck for lecture 12, what would be the resulting set of parsimonious proteins identifications How many species are in the output (3 points) 3. Using the following table of peptides mapping to proteins from the SARS-CoV-2 data Peptide sequence Proteins ASNPFLPGGGPATGPSVTNPFQPAPPATLTLNQLR sp|Q9Y6I3-3|EPN1_HUMAN sp|Q9Y6I3|EPN1_HUMAN sp|Q9Y6I3-1|EPN1_HUMAN PSTNGTTAGGFDTEPDEFSDFDRLR sp|Q9Y6I3-3|EPN1_HUMAN tr|K7EMP4|K7EMP4_HUMAN PSTNGTTAAGGFDTEPDEFSDFDR sp|Q9Y6I3-1|EPN1_HUMAN tr|K7EMP4|K7EMP4_HUMAN EEADQPPSCGPEDDAQLQLALSLSR sp|Q9Y6I3|EPN1_HUMAN NIVHNYSEAEIK sp|Q9H201-2|EPN3_HUMAN sp|Q9Y6I3-3|EPN1_HUMAN sp|Q9Y6I3|EPN1_HUMAN sp|Q9Y6I3-1|EPN1_HUMAN SPGAFDMSGVR sp|Q9Y6I3-3|EPN1_HUMAN sp|Q9Y6I3|EPN1_HUMAN sp|Q9Y6I3-1|EPN1_HUMAN ENMYAVQTLK sp|Q9Y6I3-3|EPN1_HUMAN sp|Q9Y6I3|EPN1_HUMAN sp|Q9Y6I3-1|EPN1_HUMAN LQMAIEESKR sp|Q9Y6I3-1|EPN1_HUMAN sp|Q9Y6I3|EPN1_HUMAN sp|Q9Y6I3-3|EPN1_HUMAN LQMAIEESK sp|Q9Y6I3-1|EPN1_HUMAN sp|Q9Y6I3|EPN1_HUMAN sp|Q9Y6I3-3|EPN1_HUMAN . a. Which proteins (if any) are subsumable For each subsumable protein, also indicate which other protein(s) make it subsumable. (2 points) b. Applying the maximum parsimony algorithm from slide 19 in the slide deck for lecture 12, what would be the resulting set of parsimonious proteins identifications (3 points)
