Define the planted motif search problem.
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4. Define the planted motif search problem.
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- 8. Given the following two sequences, create a pairwise alignment by hand. Do not place any gaps in the sequences to optimize alignment. Use an identity matrix and BLOSUM62 substitution matrix to create the two sets of pairwise alignments. Report the identity, identity score, similarity, and similarity score.Sequence 1: ATPL MSequence 2: ATKI MHidden 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]which substitution matrix would you choose for a BLASTP search? justify your choice.
- Briefly discuss the applications of k-mer analysis.Describe the distinguishing features of the solenoid and zigzag models13. What does the Master Mix contain? 14. What are primers? Why is a primer added? 15. Once the primers bind, what occurs next? 16. What does "highly conserved" mean? 17. Why are highly conserved regions important in this lab?
- 5. 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, SEP (2013), Ann Hum Biol 40, 463-471). (iv) There are approx. 23,800 undergraduate students at the University. SP Show your calculations in full.s5. 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.Draw a G}C base pair. Draw an A}T base pair.
- a - What is Position-Specific Scoring Matrices (PSSM) and how do we obtain it? b - Construct the HMM for the following sequences where the matches are considered for the columns that don't have any gap T G A A G T T G A I A G G C A G T G G C T A G5. 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,SEP (iii) an adult human is constructed from about 3.7 x 1013 cells (Bianconi et al, SEP (2013), Ann Hum Biol 40, 463–471). SEP (iv) There are approx. 23,800 undergraduate students at the University. SP Show your calculations in full. SEP5. 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, SEP (iii) an adult human is constructed from about 3.7 x 1013 cells (Bianconi et al, SEP (2013), Ann Hum Biol 40, 463– 471). SEP (iv) There are approx. 23,800 undergraduate students at the University.SEP Show your calculations in full. SEP
