DNA Sequence Processing and Phylogenetic Analysis

Question 1

What are the BlastN criteria?

Answer 1

1. Max score
2. Total score
3. Query cover
4. E-value
5. Max ident

Question 2

This is the highest alignment score calculated from the sum of the similarities and match/mismatch of nucleotide bases between the sample and the available sequences.

Answer 2

Max score

Question 3

This is the total alignment score of sequences available in the web

Answer 3

Total score

Question 4

This is the percentage included in the align segment

Answer 4

Query cover

Question 5

This is the number of alignments expected by chance

Answer 5

E-Value

Question 6

This is the highest percentage of identity of the line segments

Answer 6

Max identification

Question 7

This refers to the number of base pairs

Answer 7

Accession length

Question 8

This describes the arrangement of the DNA, RNA, or protein sequences

Answer 8

Sequence alignment

Question 9

This type of sequence alignment in which homology can be inferred and evolutionary relationships can be studied through phylogenetic analysis.

Answer 9

Multiple Sequence Alignment

Question 10

This type of sequence alignment identifies regions of similarity.

Answer 10

Pairwise Sequence Alignment

Question 11

This indicates that the sequence is conserved throughout the sample taxa at a particular base

Answer 11

*

Question 12

What are the two types of alignment?

Answer 12

Muscle and ClustlW

Question 13

This type of alignment aligns multiple sequences at a time

Answer 13

Muscle alignment

Question 14

This type of alignment checks all sequences at one go.

Answer 14

Muscle Alignment

Question 15

This type of alignment uses the pairwise alignment algorithm

Answer 15

ClustlW Alignment

Question 16

What is more accurate? Muscle alignment or ClustlW Alignment?

Answer 16

Muscle Alignment

Question 17

This determines relationships among sequences and traces evolutionary history.

Answer 17

Phylogenetics

Question 18

This explains how sequences evolve

Answer 18

Phylogeny

Question 19

What is the suggested number of bootstrap values for accuracy?

Answer 19

1,000

Question 20

What are the aspects of phylogenies?

Answer 20

1. Topology
2. Branches
3. Nodes
4. Root
5. Confidence

Question 21

This aspect of phylogeny covers the path of transmission of genetic information across generations.

Answer 21

Branches

Question 22

This aspect of phylogeny represents sequences/hypothetical sequences.

Answer 22

Nodes

Question 23

This aspect of phylogeny represents the most recent/common ancestor of all taxa in the tree.

Answer 23

Root

Question 24

This aspect of phylogeny refers to the bootstrap value and determines the accuracy and probability of how the tree generated is accurate.

Answer 24

Confidence

Question 25

This is usually added to easily distinguish the species and outgroup.

Answer 25

Outgroup