NAME:... MODEL ANSWER... STUDENT NUMBER:... Maximum marks: 50. Internal Examiner: Hugh Murrell, Computer Science, UKZN
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1 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 1 NAME: MODEL ANSWER... STUDENT NUMBER: Maximum marks: 50 Internal Examiner: Hugh Murrell, Computer Science, UKZN External Examiner: Ben Murrell, Dept. of Medicine, UCSD
2 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 2 Question 1 (4 marks) Describe the 4-letter alphabet employed by nature to encode an organism s genome and explain what is meant by the term reverse complement. The alphabet for DNA sequences is A, C, G, T Genetic sequences have a direction associated with them. Given a forward strand the reverse complement strand is generated by mapping: A to T, C to G, G to C and T to A and then reversing the sequence.
3 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 3 Question 2 (4 marks) 2a) A sequence of 15 independent letters is drawn from the uniform distribution on the DNA alphabet, {ACGT}. What is the probability of it coding for the amino acid sequence MPLS*? b) If there were just 2 bases in the DNA alphabet, C and G say, what would be the minimum codon length for there to be enough codons to specify the 20 amino acids and a stop codon? 5, because 2 4 = 16 which is not enough and 2 5 = 32 which is plenty.
4 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 4 Question 3 (10 marks) 3a In Pokemon genetics the symbol Y is for the dominant yellow skin, whilst y is for white recessive skin. Similarly J is for the dominant jagged tail whilst j is for the recessive straight tailed Pokemon. In the space below, draw a Punnett square for the cross: YyJj x YyJj between two doubly heterozygous Pokemon, often referred to as the Pikachu.
5 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 5 3b Using your punnet square calculate what fraction of offspring from Pikachu Pokemon couples will be: a. Yellow b. Straight tail c. White and straight tail d. Yellow and straight tail e. Yellow and jagged tail f. Pikachu Write your answers next to each item above. a. 12/16 Yellow b. 4/16 Straight tail c. 1/16 White and straight tail d. 3/16 Yellow and straight tail e. 9/16 Yellow and jagged tail f. 4/16 Pikachu
6 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 6 Question 4 (8 marks) 4a (2 marks) Which of the following strings match the regular expression: a*bb(ab ba)* a. abb b. abba c. aaba d. bbbaab e. bbababbab 4b (6 marks) Study the expression: ATG(?:[ATGC]3(?<!TAG TAA TGA))13,(?:TAG TAA TGA) In the space below, explain why this regular expression could be useful in bioinformatics and give a description in English of what each part of the expression accomplishes. 4a. item a and d 4b. This is for recognising open reading frames. start with an ATG follow up with codons of length 3 no stop codon in the next 13 codons end with a stop codon after codon 14
7 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 7 Question 5 (8 marks) In the DNA strand shown below there are four Open Reading Frames, two on the forward strand and two on the reverse strand. Find them and translate them to amino acid sequences using the standard genetic code attached to this test paper. 5 AGCGCTTACTCAGGCATGGGGATGACCCCGCGACTTGGATTAGAGTCTCTTTTGGAATAAGCCATGTCTCAG 3 MGMTPRLGLESLLE, MTPRLGLESLLE, MAYSKRDSNPSRGVIPMPE, MPE
8 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 8 Question 6 (10 marks) Study the Needleman-Wunsch global alignment algorithm attached to this test paper. 6a) Using the following scoring scheme and the empty scoring and traceback tables on the following page, perform a global alignment computation for the two sequences GAATTCTCCT and GATTACC. match +2 mismatch -1 gap -2 6b) In the space below write down an optimal global alignment and re-compute its score using the parameters above. G A A T T C T C C T G - A T T - A C C - Score: (6 2) (3 2) (1 1) = 5
9 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 9 Scoring Table G A A T T C T C C T G A T T A C C Traceback Table G A A T T C T C C T 0 G X A < X T X T X < A X C X C X <
10 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 10 Question 7 (6 marks) Explain what is meant by an Affine Gap penalty scheme and indicate how you would change the Needleman-Wunsch global alignment algorithm attached to this test paper in order to accommodate Affine Gap penalty parameters.
11 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 11 Extra space if you need it
12 COMP710, Bioinformatics with Julia, Test One, Thursday the 20 th of April, 2017, 09h30-11h30 12 Attachments Standard genetic code: TTT F Phe TCT S Ser TAT Y Tyr TGT C Cys TTC F Phe TCC S Ser TAC Y Tyr TGC C Cys TTA L Leu TCA S Ser TAA * Stp TGA * Stp TTG L Leu TCG S Ser TAG * Stp TGG W Trp CTT L Leu CCT P Pro CAT H His CGT R Arg CTC L Leu CCC P Pro CAC H His CGC R Arg CTA L Leu CCA P Pro CAA Q Gln CGA R Arg CTG L Leu CCG P Pro CAG Q Gln CGG R Arg ATT I Ile ACT T Thr AAT N Asn AGT S Ser ATC I Ile ACC T Thr AAC N Asn AGC S Ser ATA I Ile ACA T Thr AAA K Lys AGA R Arg ATG M Met ACG T Thr AAG K Lys AGG R Arg GTT V Val GCT A Ala GAT D Asp GGT G Gly GTC V Val GCC A Ala GAC D Asp GGC G Gly GTA V Val GCA A Ala GAA E Glu GGA G Gly GTG V Val GCG A Ala GAG E Glu GGG G Gly Needleman-Wunsch algorithm (Global alignment)
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