Lecture 2 - RH Flashcards Preview

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Flashcards in Lecture 2 - RH Deck (23):
1

What is BLAST used for?

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

2

What is the output of a BLAST search?

A pairwise alignment

3

What is found using BLAST searches?

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

4

What are some uses for BLAST?

Study evolution

Discover function

Find crucial features (motif finding)

Identify causes of disease (detect variable sites in alignment)

5

What is homology?

Genes or proteins are homologous if they share a common ancestor

6

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

Homology (common ancestor)

Orthology (Descent from speciation)

Paralogy (Duplication event causes separate evolution)

Xenology (Horizontal transfer event)

7

When are proteins said to be homologous?

>25% identical aas (likely)

18 - 25% twilight zone (needs further investigation)

8

How is a pairwise alignment interpreted?

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

9

Which is more informative; protein or DNA sequences?

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

10

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

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

11

What are the types of alignments?

Uniformative (in exercise book)

Ungapped alignment ("""")

Gapped alignment ("""")

12

Why are gapped alignments used?

It is more maleable due to accounting for frameshift mutations

13

What BLAST tools are available on NCBI?

Nucleotide BLAST

Protein BLAST

Translated BLAST

Genome BLAST

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

14

What is the difference between global and local alignments?

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

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

15

What is dynamic programming?

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.

16

Why is dynamic programming used in alignments?

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

17

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

Initialization

Scoring the matrix

Traceback

18

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

a large penalty is applied to the score

19

What is a PAM?

Point Accepted Mutation

*Number of changes/100 amino acids

20

Which matrices are used by BLAST?

BLOSUM matrices

21

When is BLOCKS used?

For conserved motifs

22

What does the number after BLOSUM represent?

Percentage identity based on observed alignments

23

What are the penalties applied by BLOSUM62 matrix?

Opening a new gap = -11
Extending a gap = -1