Part 2 - Lecture 2 - Local Pairwise Sequence Alignment

Question 1

Why local alignment?

Answer 1

we often do not know which parts of two sequences we should align

Question 2

Why might parts of interesting sequences be more important to certain functions?

Answer 2

1. genic vs intergenic parts of a traditional gene locus
2. exons vs introns within a gene - exons are what remains after splicing since some exons are noncoding
3. proteins have disordered parts vs domains with secondary structures

Question 3

Is there such a thing as junk DNA?

Answer 3

tough to claim any part of genome has no function so NO

Question 4

If we have two sequences which are i.i.d., what amount can we expect for the two sequences to match?

Answer 4

25%

Question 5

What is the local alignment?

Answer 5

the best glocal alignment taken from all substrings

Question 6

What is the smith-waterman recurrence?

Answer 6

instead of putting a negative penalty value put a zero
-this makes all base cases start at zero

Question 7

In organizing mismatch scores why do we penalize transitions less than transversions?

Answer 7

cause purine to purine and pyrimidine to pyrimidine is more common(transition) than purine to pyrimidine or pyrimidine to purine (transversion)

Question 8

How does the Smith-waterman algorithm depend on sensible scoring?

Answer 8

• the zero point is critical
  -positive scoring alignments must be good
  -negative scoring alignments assumed not useful

Question 9

Question 10

In local alignment, what is added?

Answer 10

1. a zero to appear for a rest which changes the base cases
2. start the traceback at the highest value
3. stop the traceback once you hit zero