The alignment that has a higher score according to identity-based alignment scoring. Concept introduction: Identity−based alignment scoring is a method to score the identical alignments present in a sequence. The identical amino acids are added while the gaps in the sequence are subtracted to determine the identical score.

Question

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…

Answer 1

Question

Chapter 6, Problem 3P

Interpretation Introduction

Interpretation:

The alignment that has a higher score according to identity-based alignment scoring.

Concept introduction:

Identity−based alignment scoring is a method to score the identical alignments present in a sequence. The identical amino acids are added while the gaps in the sequence are subtracted to determine the identical score.

Interpretation Introduction

(b)

Interpretation:

The alignment that has a higher score according to the Blosum -62 substitution method.

Concept introduction:

Blosum-62 is a type of substitution matrix that is used to score the replacement of amino acids. A positive score of substitution matrix indicates that substitution of amino acid occurs more frequently while a negative score is rare for substitutions.

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