Lecture 8 Multiple Alignment

Question 1

Homology

Answer 1

similarity that is the result of inheritance from a common ancestor

Question 2

Orthologs

Answer 2

genes in different species that evolved from a common ancestral gene by speciation. Normally, orthologs retain the same function in the course of evolution.

Question 3

Paralogs

Answer 3

genes related by duplication within a genome. paralogs evolve new functions, even if these are related to the original one.

Question 4

An Alignment

Answer 4

an hypothesis of positional homology between bases or amino acids.

Question 5

Homology versus Similarity

Answer 5

• When two sequences are descended from a common evolutionary origin, they are homologous. When thinking of homology remember pregnancy
• sequence similarity is the percentage of aligned residues that are similar in physiochemical properties (size, charge, and hydrophobicity).
• Sequence similarity can be quantified using percentages (40% similarity); homology is a qualitative statement (homologous or nonhomologous).

Question 6

What are other set of related terms for sequence comparison

Answer 6

sequence similarity and sequence identity.

Question 7

Sequence Identity

Answer 7

the percentage of matches of the same amino acid residues between two aligned sequences.

Question 8

what are sequence similarity and sequence identity synonymous for

Answer 8

nucleotide sequences.

Question 9

Sequence identity can be calculated in two different ways

Answer 9

1)I=[(Li ×2)/(La +Lb)]×100
La and Lb are the total lengths of each individual sequence.
Li is the number of aligned identical residues.

2) I(S)% = Li/La
where La is the length of the shorter of the two sequences.

Question 10

What issues are associated with multiple sequence alignments

Answer 10

All sequences show some similarity (even random sequences, 25% for nucleotides, 5% for proteins).

Similarity levels might be high in some parts of the sequence and low in other parts.

Sequences might show substantial length variation and presence/absence of various domains.

Question 11

What are the 3 main methods of alignment:

Answer 11

• Manual
• Automatic
• Combined

Question 12

Why might manual alignment be carried out ?

Answer 12

– Alignment is easy.
– There is some extraneous information (structural).
– Automated alignment methods have encountered
the local minimum problem.
– An automated alignment method can be “improved”.

Question 13

Progressive Alignment

Answer 13

a heuristic method and as such is not guaranteed to find the ‘optimal’ alignment.

Devised by Feng and Doolittle in1987.

Question 15

What steps are involved in the ClustalW procedure

Answer 15

1. Quick pairwise alignment: calculate distance matrix
2. Neighbor-joining tree (guide tree)
3. Progressive alignment following guide tree

Question 16

How is the ClustalW Pairwise Alignment done?

Answer 16

• First perform all possible pairwise alignments between each pair of sequences.
• Calculate the ‘distance’ between each pair of sequences based on these isolated pairwise alignments.
• Generate a distance matrix.

Question 17

What is the Neighbor-joining method

Answer 17

*The neighbor-joining method is a greedy heuristic which joins at each step, the two closest sub-trees that are not already joined.

*One of the important concepts in the NJ method is neighbors, which are defined as two taxa that are connected by a single node in an unrooted tree

Question 18

Multiple Alignment- First pair

Answer 18

• Align the two most closely-related sequences first.
• This alignment is then ‘fixed’ and wil lnever change. If a gap is to be introduced subsequently, then it will be introduced in the same place in both sequences, but their relative alignment remains unchanged.

Question 19

What are the advantages and disadvantages of ClustalW

Answer 19

• Advantages:
  – Speed.
• Disadvantages:
  – No objective function.
  – No way of quantifying whether or not the alignment is good
  – No way of knowing if the alignment is ‘correct’.