Chapter 5-Bioinformatics

Question 1

Explain the molecular clock hypothesis

Answer 1

1. Mutations accumulate randomly over time and there is a relatively constant rate of mutation of N base pairs per year
2. Most of the mutations are neutral are natural selection would neither favour or disfavour them
3. When an individual has progeny, these mutations are passed on to the next generation.
4. Genetic difference between any two species is proportional to the time since these species last shared a common ancestor

Question 2

What is the mutation rate in humans?

Answer 2

0.5-1 mutations/ 1 gigabasepair in one generation

Question 3

Define homologues

Answer 3

Homologues are sequences that share a common evolutionary history (originated from a common ancestor)

Question 4

Define orthologues

Answer 4

Sequences in different species that arose from a common ancestral gene during speciation and are responsible for the same function

Question 5

Define paralogs

Answer 5

Homologous sequences within a single species that arose by gene duplication

Question 6

Define sequence alignment

Answer 6

Process of lining up 2 or more sequences to achieve maximal levels of identity for the purpose of assessing the degree of similarity and the possibility of homology

Question 7

Functions of pairwise sequence alignment

Answer 7

1. Identify common and differing aa/nucleotides in equal positions
2. Identify domains or motifs shared between proteins
3. Evaluate if two proteins or genes have a similar sequence

Question 8

Difference between pairwise sequence and multiple sequence

Answer 8

Pairwise: compares 2 sequences
Multiple: compares 3 or more sequences

Question 9

What is local sequence alignment

Answer 9

• optimal similarity scores of 2 sequences determined over numerous subregions along the length of the 2 sequences
• useful in identifying protein domains

Question 10

What is global sequence alignment

Answer 10

• optimal similarity score is determined over the entire length of the 2 sequences
• useful in assessing whether genes or proteins are homologous

Question 11

How to calculate alignment score

Answer 11

Alignment score= match scores + gap penalties + mismatch scores

-gap penalties and mismatch scores have negative values

Question 12

What is Needleman-Wunsch alignment?

Answer 12

Global sequence alignment

Question 13

What is the Smith-Waterman alignment?

Answer 13

Local alignment

Question 14

What do the values assigned to PAM mean?

Answer 14

• refers to the number of aa substitutions per 100 aa

Question 15

PAM family extrapolation formla

Answer 15

PAM-n=(PAM-1)^n

Question 16

PAM vs BLOSUM

Answer 16

1. PAM matrices are based on global alignments of closely related proteins while BLOSUM matrices are based on local alignments
2. All PAM matrices are extrapolated from PAM-1 while all BLOSUM matrices are based on observed alignments

Question 17

Arrange the following in increasing order of divergence

BLOSUM-62, BLOSUM-45, BLOSUM-80

Answer 17

BLOSUM 80, BLOSUM 62, BLOSUM 45

Question 18

How should you choose the appropriate aa substitution matrix?

Answer 18

• expected degree of sequence divergence

Question 19

Which algorithms are exact?

Answer 19

Needleman-Wunsch and Smith-Waterman

-optimal but time consuming to compute

Question 20

Which alignment algorithms are heuristic methods?

Answer 20

Pairwise: BLAST
Multiple alignment: all widely used multiple alignment programmes e.g. MAFFT
- based on common sense and assumptions
- not optimal, but fast

Question 21

Function of BLAST

Answer 21

• a heuristic local alignment programme
• allows scientists to compare new sequences with databases containing many characterised genes
• results can provide valuable functional and evolutionary info

Question 22

How to interpret the E-vale in BLAST

Answer 22

• statistical interpretation of how likely it is to get the alignment score by chance
• smaller E indicates a more significant alignment
• E<0.02 seq is probably homologous
• 0.021 this match is probably by chance

Question 23

Importance of multiple sequence alignment

Answer 23

1. Links proteins at the aa level, making it possible to identify conserved features, predict functionally impt residues and identify locations which affect the biochemical properties of the protein
2. Basis for phylogenetic tree construction
3. Allows generalisation of sequences to profiles

Question 24

Uses of phylogeny

Answer 24

1. Identifying orthologs and paralogs in gene families
2. Discover population history and species history
3. Estimate divergence times assuming molecular clock

Question 25

Problem with multiple sequence alignment and how it can be overcome

Answer 25

• high dimensionality of solution space—> makes optimal solution hard to calculate with dynamic programming
• solution: use iterative algorithms

Question 26

Steps in CLUSTAL

Answer 26

1. Calculate pairwise alignments for every sequence pair and calculate sequence distances
2. Using distances, estimate a guide tree using neighbour joining
3. Using the guide tree, align the sequences in that order

Question 27

Steps in neighbour-joining

Answer 27

1. Find 2 nodes with minimal relative distance from each other compared to the distance to the others
2. Replace these 2 nodes with a common ancestral node
3. Compute all pairwise distances between the remaining node and the ancestral node
4. Repeat steps 1-3 until only 2 nodes remain and connect them with an edge

Question 28

Types of multiple sequence alignments

Answer 28

Progressive and iterative