Lecture 2 - RH

Question 1

What is BLAST used for?

Answer 1

To search for sequences by typing those sequences in the search bar

Question 2

What is the output of a BLAST search?

Answer 2

A pairwise alignment

Question 3

What is found using BLAST searches?

Answer 3

Relatives can be found using BLAST.

BLAST can check whether a protein encodes:

• Known protein with known function
• Known protein unknown function
• Unknown protein known function (familiar functional domains)
• Unknown protein unknown function

Question 4

What are some uses for BLAST?

Answer 4

Study evolution

Discover function

Find crucial features (motif finding)

Identify causes of disease (detect variable sites in alignment)

Question 5

What is homology?

Answer 5

Genes or proteins are homologous if they share a common ancestor

Question 6

What are the types of “ologies” hat can exist between proteins or nucleotides?

Answer 6

Homology (common ancestor)

Orthology (Descent from speciation)

Paralogy (Duplication event causes separate evolution)

Xenology (Horizontal transfer event)

Question 7

When are proteins said to be homologous?

Answer 7

> 25% identical aas (likely)

18 - 25% twilight zone (needs further investigation)

Question 8

How is a pairwise alignment interpreted?

Answer 8

Choose 2 sequences

Select algorithm that generates score

Allow gaps (insertions/deletions)

Score reflects similarity

Alignments can be global or local

Probability that the alignment occured by chance is estimated

Question 9

Which is more informative; protein or DNA sequences?

Answer 9

Protein:

It contains 20 rather than 4 characters

Codons are degenerate

Protein sequences offer a longer “look-back” time

DNA sequences can be converted into protein sequences and used in pairwise alignments

Question 10

Why are DNA alignments used if protein alignments are more accurate?

Answer 10

To identify cDNA, non-coding regions of DNA, and to identify DNA polymorphisms

Question 11

What are the types of alignments?

Answer 11

Uniformative (in exercise book)

Ungapped alignment (“”””)

Gapped alignment (“”””)

Question 12

Why are gapped alignments used?

Answer 12

It is more maleable due to accounting for frameshift mutations

Question 13

What BLAST tools are available on NCBI?

Answer 13

Nucleotide BLAST

Protein BLAST

Translated BLAST

Genome BLAST

smart BLAST (can be used to create a phylogenetic tree)

Question 14

What is the difference between global and local alignments?

Answer 14

Global alignment: Aligns all of 2 sequences and finds global similarity

Local alignment: Looks for regions of similarity. (99% of cases)

Question 15

What is dynamic programming?

Answer 15

Dynamic programming (usually referred to as DP ) is a very powerful technique to solve a particular class of problems. It demands very elegant formulation of the approach and simple thinking and the coding part is very easy.

Question 16

Why is dynamic programming used in alignments?

Answer 16

Finding optimal alignments is a computationally difficult task so problem is divided into states and for each state a decision is made

Question 17

What are the 3 steps of dynamic programming for sequence alignments?

Answer 17

Initialization

Scoring the matrix

Traceback

Question 18

What happens to similarity score when a gap is introduced or extended?

Answer 18

a large penalty is applied to the score

Question 19

What is a PAM?

Answer 19

Point Accepted Mutation

*Number of changes/100 amino acids

Question 20

Which matrices are used by BLAST?

Answer 20

BLOSUM matrices

Question 21

When is BLOCKS used?

Answer 21

For conserved motifs

Question 22

What does the number after BLOSUM represent?

Answer 22

Percentage identity based on observed alignments

Question 23

What are the penalties applied by BLOSUM62 matrix?

Answer 23

Opening a new gap = -11

Extending a gap = -1