Lecture 3

Question 1

Procedue of comparing two or more sequences by searching for a series of individual characteris that are in the same order in the sequence

Answer 1

Sequence Alignment

Question 2

Significance of Sequence Alignment

Answer 2

• a way to learn about a gene or protein
• discover functional, structural and evol. information

Question 3

process of lining up two sequences to achieve maximal levels of identity and show conservation of residues

Answer 3

pairwise sequence alignment

Question 4

used to assess degree of similarity and possibly homology

Answer 4

Pairwise sequence alignment

Question 5

term thats refers to the same residues between two proteins; may be in global or local alignment

Answer 5

Identical

Question 6

term that referes to residues have structural or functional related; can only use “higher/lower degree of similarity”

Answer 6

Similar

Question 7

sum of both identical and similar residues; goal of pairwise alignment

Answer 7

Percent similarity

Question 8

Calculating percent similarity, steps

Answer 8

1. Count the number of sequence in matching positions
2. Count number of aligned positions
3. Divide matching by total # of aligned
4. Multiply by 10

Question 9

Formula for percent similarity

Answer 9

Percent Similarity = (Number of matching position / total # of aligned position ) x 100

Question 10

Refers to the exact match between two nucleotide or amino acids

Answer 10

Identity

Question 11

refers to a resemblance between two residues that is greater than one would expect at random

Answer 11

Similarity

Question 12

• Simple fraction of identical residues
• genetic distances based on models of DNA sequence evolution

Answer 12

Nucleotide sequences

Question 13

Genetic distances based on models of AMINO ACID sequence evolution
- measured using matrices

Answer 13

Peptide sequences

Question 14

Example of matrices used to measure peptide sequences

Answer 14

• PAM
• BLOSUM

Question 15

a sequences that share a common evolutionary ancestry

Answer 15

Homologous sequences

Question 16

sequence regions that are homologous are also called _____

Answer 16

Conserved

Question 17

share a common evolutionary ancestry

Answer 17

Homologs

Question 18

derived from a single ancestral gene in the Least Common Ancestor

Answer 18

Orthologous genes

Question 19

two or more homologous genes found within a single species

• duplicated genes with the some genome, may evolve new function

Answer 19

Paralogous Genes

Question 20

Two types of pairwise comparison

Answer 20

• Graphical analysis
• Residue/Residue analysis

Question 21

Example of Graphical Analysis

Answer 21

Dot plot matrix

Question 22

Types of Residue/Residue analysis

Answer 22

1. Global Alignment
2. Local alignment

Question 23

• visually compares two sequences (like DNA, RNA, or protein) on a 2D grid, placing a dot for each matching character to highlight similarities and identify repeats, insertions, or deletions through graphical pattern

Answer 23

Dot Plot

Question 24

• Compares the sequences as a whole
• analyzes polymorphism between closely related sequences

Answer 24

Global Sequences Alignment

Question 25

What algorithm does Global sequence alignment use?

Answer 25

Needleman-Wunch algorithm

Question 26

uses dynamic programming equations to align sequences - aims to align all sites optimally within the sequences

Answer 26

Needleman-Wunsch algorithm (1970)

Question 27

stretches of sequences with high density of matches are aligned - detect similar subsequences in two sequences

Answer 27

Local alignment

Question 28

algorithm that is used in Local alignment

Answer 28

- Smith-waterman Algorithm

Question 29

the algorithm based on high-scoring local match - identify all possible subsequences of 2 sequences

Answer 29

Smith-waterman algorithm

Question 30

is used in sequence alignment to assign numerical values to matches, mismatches, and substitutions.

Answer 30

Scoring matrix

Question 31

types of substitution (scoring) matrices used in sequence alignment

Answer 31

- PAM (Percent Accepted Mutation) - BLOSUM-X (Blocks Amino Acid Substitution Matrix)

Question 32

Derived from observed evolutionary mutations in closely related proteins. - Estimates the rate at which each possible residue in a sequence changes to each other resider over time

Answer 32

PAM

Question 33

- Derived from conserved sequence blocks in protein families. - Designed to find both close and distant sequence relationship

Answer 33

BLOSUM

Question 34

Different pairwise alignment Software

Answer 34

- ClustalW2/ ClustalOmega - TCoffee - JAligner - BLAST

Question 35

Early version for multiple sequence alignment

Answer 35

ClustalW2

Question 36

Modern, improved version of ClustalW2; handles large datasets efficiently.

Answer 36

ClustalOmega

Question 37

- Produces highly accurate multiple sequence alignments. - Combines results from different alignment methods for better quality.

Answer 37

TCoffee

Question 38

an algorithm for rapid searching of nucleotide and protein databases

Answer 38

Basic Local Alignment Search Tool

Question 39

Applications of Blast

Answer 39

- Sequence Identification - Determine homologs - Determine proteins or genes - Gene discovery - Discover variants of gene or protein - Investigate alternative splice sites

Question 40

Types of BLAST Variants

Answer 40

- blastp - blastn - blastx - tblastn - tblastx

Question 41

use to compare a protein query to a data base of proteins

Answer 41

blastp

Question 42

use to compare both strands of DNA query against DNA data base

Answer 42

blastn

Question 43

translates a DNA sequence into six protein sequences using all six possible reading frames, and then compares "each of these" proteins to a protein databse

Answer 43

blastx

Question 44

used to translate every DNA sequence in a database into six potential proteins, and the compare "your protein query" against each of those translated proteins

Answer 44

tblastn

Question 45

is the most computational intensitive BLAST algorithm. - translates DNA from both a query and data base into six potential protein

Answer 45

tblastx

Question 46

What doe E-value represent in blast result

Answer 46

- evaluates the statistical significance of a BLAST alignment.

Question 47

the E-value taht is considered the cuttoff point

Answer 47

E=10^-4

Question 48

The E-value which means that the two sequences are statistically identical

Answer 48

E=0