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- Using the Dynamic Programming algorithm for pairwise local alignment we covered in class, construct the dynamic programming score table for a local alignment of the following two sequences, using the following scoring parameters: match score = +5, mismatch score = -3, gap penalty = -2.: ACGTATCGCGTATA GATGCTCTCGGAAAWhat is score of the best local alignment between these two sequences? Show the alignment of these sequences. asapCalculate the dynamic programming matrix and the optimal local and global alignment for the DNA sequences a: GAATTC and b: GATTA, scoring +2 for a match, -1 for a mismatch, and using a linear gap penalty function WL) = -2L thank youHidden Markov Model (HMM) Construct the HMM for the following sequences 2) G C A A A A G A A T G C A A G A The matches are considered for the columns [1, 2,4,5, and 7]
- Compute the percent identity of the following pairwise sequence alignment: -TGAGACTTAGAGT |..|... | | | | | ATAGGAGCGAGAGTwhich substitution matrix would you choose for a BLASTP search? justify your choice.In hybridizing microarrays, we use a solution that contains {3X SSC, 0.5% SDS, 5ug/ml salmon sperm DNA, 5% glycerol}. Describe how to make 100ul of this solution using stocks of 20X SSC, 10% SDS, and 10 mg/ml salmon sperm DNA, sheared, in water. Note that Molecular Biology Grade H2O must be used in making up this solution.
- Rice genome contains 30% C on a molar basis. What are the mole percentages of A, G, and T?Given the fact that 1 fg of DNA = 9.78 * 105base pairs (on average), you can convert the amount of DNA per cell to the lengthof DNA in numbers of base pairs. (a) Calculate the number of basepairs of DNA in the haploid yeast genome. Express your answer inmillions of base pairs (Mb), a standard unit for expressing genomesize. Show your work. (b) How many base pairs per minute weresynthesized during the S phase of these yeast cells?Calculate the number of clones required to obtain with a probability of 0.99 a specifi c 5-kb fragment from C. elegans (Table).
- List and Describe the algorithm of BLOSUM substitution matrix computation.A light year is approximately 9.46 x 1012 kilometres. Calculate in light years, the approximate total length of DNA in all the undergraduate students studying at Cardiff University given that: (i) the human haploid genome comprises approx. 3.2 x 109 base-pairs (bp) DNA; (ii) 10 bp of DNA has a length of approx. 3.4 nm, (iii) an adult human is constructed from about 3.7 x 1013 cells (Bianconi et al, (2013), Ann Hum Biol 40, 463–471). (iv) There are approx. 23,800 undergraduate students at the University. Show your calculations in full.Below are 9 possible primer pairs. ● Determine which primer pair is the best choice by considering the following: 1. primers should be 18-24 bases in length; 2. base composition should be 45-55% (G+C); 3. primers should end (3') in a G or C, or CG or GC: this prevents "breathing" of ends and increases efficiency of priming; 4. Tms tween 55-70°℃ are preferred (Tas, annealing temperatures, are approximately 5°C lower than the Tm); 5. the Tm for your primer pair should be within 2 degrees of each other, though ideally the same; 6. runs of three or more Cs or Gs at the 3'-ends of primers may promote mispriming at G or C-rich sequences (because of stability of annealing), and should be avoided; 7. 3'-ends of primers should not be complementary (i.e. base pair), as otherwise the formation of primer dimers will result; 8. primer self-complementary (ability to form secondary structures such as hairpins) should be avoided. • Explain why the other primers are not good choices. ● Underline or…