Introduction to sequence analysis

Question 1

What is a global sequence alignment?

Answer 1

• sequence comparison along the entire length of the two sequences being aligned
• best for high-similar sequences of similar length
• as the degree of sequence similarity declines, global alignment methods tend to miss important biological relationships

Question 1

Character based methods for building a phyologenic tree

Answer 1

• ML (maximum likelyhood)
• MP (maximum parsimony)

Question 2

Define the terms homology and homologs

Answer 2

Homlogoly - The presence of a similar feature because of descent from common ancestor (defines evolutionary relationships)

Homologs - Genes either are or are not homologous (not measured in degrees)

Question 3

3 widely used MSA programs

Answer 3

• Claustal-W
• T-COFFEE
• MAFFT

Question 4

Why do we perform sequence analysis?

Answer 4

• discover function
• study evolution
• find crucial features
• identify cause of disease

Question 4

What is a speciation event?

Answer 4

Speciation is a lineage-splitting event that produces two or more separate species

Question 5

What does the p-value of an alignment mean?

Answer 5

It tells us about the probability that we get an alignment with this score by chance. Should be close to zero

Question 6

What is a taxon?

Answer 6

A set or group of organisms, most often species, at the end of a branch

Question 8

What is taken into consideration when scoring two aligned sequences?

Answer 8

• The kind of AA
• the chemical properties of the AAs

Question 8

Why do we do multiple alignments?

Answer 8

• to identify conserved regions, patterns, and domains
• to identify new members of protein families
• to predict structure and function of new protein sequences
• as a preliminary step in molecular evolution analysis using phylogenetic methods for constructing phylogenetic trees

Question 8

What is a clade?

Answer 8

A group of organisms that includes an ancestor and all descendants of that ancestor, irrespective of how closely they may or may not resemble one another

Question 10

What kind of alignment does BLAST perform?

Answer 10

A local sequence alignment

Question 11

Distance based methods for building a phylogenic tree

Answer 11

• UPGMA (unweighted pair group method with arithmetic mean)
• NJ (neighbor joining)

Question 12

I want to compare sequences of different lenghts, which alignment should I use?

Answer 12

Local sequence alignment

Question 12

My two sequences are really similar and also have about the same length. Which alignment should I use?

Answer 12

Global sequence alignment

Question 13

What does the E-value of an alignment tell us?

Answer 13

It tells us how many times (or how many sequences) we expect such an alignment with this score by chance.

Question 14

What is a local sequence alignment?

Answer 14

• sequence comparisons intended to find the most similar regions in the two sequences being alligned
• regions outside the area of local alignment are excluded
• more than one local alignment could be generated for any two sequences being compared
• best for sequences that share some similarity, or for sequences of different lengths

Question 15

What does “character-based methods” of phyologenic tree building mean?

Answer 15

Use the aligned characters, such as DNA or protein sequences, directly during tree inference

Question 17

Definition of homology

Answer 17

the presence of a similar feature because of descent from a common ancestor (defines evolutionary relationships)

Question 18

Definition of orthologs

Answer 18

Homologs in different species that perform the same function most likely have the same domain and 3D structure can be used to predict gene function in novel genes

Question 20

Which are the two major scoring systems used for proteins?

Answer 20

• PAM/Dayhoff
• BLOSUM series (Blocks Substitution Matrix)

Question 21

What does “distance-based methods” of phyologenic tree building mean?

Answer 21

Transform the sequence data into pairwise distances (dissimilarities), and then use the matrix during tree building

Question 23

Definition of paralogs

Answer 23

Homologs in the same species that most likely have different functions “homologs that diverged after gene duplication” provides insight into “evolutionary innovation” Gene A duplicates to gene A’ –> no evolutionary pressure on A’ because there is already a gene performing the task, so it can take on new functions

Question 24

Who do you perform phyolgeny at the end of a MSA?

Answer 24

A phyologenic tree is used to help represent evolutionary relationships between genes, proteins, and also organisms that are believed to have some common ancestry

Question 25

What does BLAST stand for?

Answer 25

Basic Local Alignment Search Tool

Question 26

State “true” or “fals” for each alternative

a) human and mouse histamine 1R are orthologs
b) Human HRH1 and Human HRH2 are paralogs
c) Orthologs and paralogs are homologs

Answer 26

All are true

Question 27

What is a root?

Answer 27

A basal node

Question 28

What is a node?

Answer 28

A common ancestor / the point at which branches connect

Question 29

What are branches?

Answer 29

Lines within the tree

Question 30

What is a cluster?

Answer 30

A cluster is a group of things placed togehter on the basis of their resemblence to one another, irrespective of their evolutionary relationship