Sequence Alignment (short ver)

Question 1

aligns two or more sequences to highlight their similarity, inserting a small number of gaps into each sequence (usually denoted by dashes) to align wherever possible identical or similar characters.

Answer 1

Basic Sequence Alignment Algorithm

Question 2

Why compare biological sequence?

Answer 2

to obtain functional or mechanistic insight about a sequence by inference from another potentially better characterized sequence
to find whether two (or more) genes or proteins are evolutionary-related
to find structurally or functionally similar regions within sequences

Question 3

practical applications of sequence alignment include…

Answer 3

similarity searching of databases
assembly of sequence reads
mapping sequencing reads to a known genome

Question 4

Protein structure prediction, annotation, etc…

Answer 4

similarity searching of databases

Question 5

reads into a longer construct such as a genomic sequence

Answer 5

assembly of sequence reads

Question 6

looking for differences from reference genome - SNPs, indels

Answer 6

resequencing

Question 7

mapping transcription factor binding sites via

Answer 7

ChiP-Seq (chromatin immuno-precipitation sequencing)

Question 8

arguably the most fundamental operation of bioinformatics

Answer 8

Pairwise sequence

Question 9

sequence comparison is most informative when it detects _

Answer 9

homologs

Question 10

sequences that have common origin; they share a common ancestor

Answer 10

homolog

Question 11

homologous sequences may either be:

Answer 11

orthologs or paralogs

Question 12

True or False: orthologs and paralogs are an example of all or nothing relationships

Answer 12

True

Question 13

Any pair of sequences may share a certain level of:

Answer 13

identity and/or similarity

Question 14

Orthologs tend to have ____ while Paralogs tend to have ______

Answer 14

Orthologs - similar function
paralogs - slightly different function

Question 15

homolog produced by speciation that have diverged due to divergence of the organisms they are associated with.

Answer 15

orthologs

Question 16

homologs produced by gene duplication

Answer 16

paralogs

Question 17

ortho is a greek word that means

Answer 17

straight; implies direct descent

Question 18

they represent genes derived from a common ancestral gene that duplicated within an organisms and then subsequently diverged by accumulated mutation

Answer 18

paralogs

Question 19

greek word meaning along side of

Answer 19

para

Question 20

Why is determining orthologs vs. paralogs can be a complex problem?

Answer 20

gene loss after duplication
lack of knowledge of evolutionary history
weak similarity because of evolutionary distance

Question 21

True or False: Homology implies exact same functions

Answer 21

False;

homology does not imply exact same functions

Question 22

may have similar function at very crude level but play a different physiological role

Answer 22

homology

Question 23

three types of sequence change that can occur during evolution

Answer 23

mutations/substitutions
deletions
insertions

Question 24

great tools to visualize sequence similarity and evolutionary changes in homologous sequences

Answer 24

alignment

Question 25

represent mutations/substitutions

Answer 25

mismatches

Question 26

represent insertions and deletions

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gaps

Question 27

one way to judge alignment is to:

Answer 27

compare their number of: matches insertions deletions mutationd

Question 28

reflect biological or statistical observations about the known sequences, and are frequently represented by scoring matrices

Answer 28

alignment scoring schemes

Question 29

if x1 and y1 is a match

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reward

Question 30

if x1 and y1 is a mismatch

Answer 30

penalty

Question 31

if either x1 and y1 is a gap

Answer 31

penalty

Question 32

the gap penalty is denoted as

Answer 32

g

Question 33

true or false: biologist often prefer parsimonious alignment

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true

Question 34

number of postulated sequence changes is minimized

Answer 34

parsimonious alignment

Question 35

True or false: there may be more than one optimal alignment and these may not reflect the true evolutionary history of our sequences

Answer 35

True

Question 36

two commonly quoted matrices for pairs of aligned sequences

Answer 36

Sequence identity sequence similarity

Question 37

typically quotes the percent of identical characters in the aligned region of two sequences

Answer 37

sequence identity

Question 38

typically, the score resulting from optimal pairwise alignment (there is dependence in parameters used like scoring scheme)

Answer 38

sequence similarity

Question 39

True or False: homology is not an all or nothing relationship, you can not have a percent homology

Answer 39

False; | homology is an all or nothing relationship

Question 40

True or False; homology is an all or nothing relationship, you can have a percent homology

Answer 40

False | you can not have a percent homology

Question 41

frequently used as an indicator of homology

Answer 41

high sequence similarity

Question 42

use to find genes and/or proteins with potentially similar or identical function

Answer 42

high sequence similarity

Question 43

can query a database of sequence by performing a series of pairwise alignments

Answer 43

high sequence similarity

Question 44

way of arranging the primary sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequence

Answer 44

sequence alignment

Question 45

aligned sequences of nucleotide or amino acid residues are typically represented as ____ within a matrix

Answer 45

rows

Question 46

inserted between the residues so that residues with identical or similar characters are aligned in successive columns

Answer 46

gaps

Question 47

True or False; alignment can also be not an exact match

Answer 47

True

Question 48

True or False: Alignment can be based on edit distance

Answer 48

True

Question 49

True or False: Alignment is usually based on a similarity measure

Answer 49

True

Question 50

the number of changes requires to change one sequence into another is called the __

Answer 50

edit distance

Question 51

every character in the query (source) string lines up with a character in the target string

Answer 51

Global alignment

Question 52

attempt to align every resiue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size

Answer 52

global alignment

Question 53

may require gap (space) insertion to make strings the same length

Answer 53

global alignment

Question 54

a general global alignment based on dynamic programming

Answer 54

Needleman Wunsch algorithm

Question 55

Needleman-Wunsch algorithm is based on

Answer 55

dynamic programming

Question 56

an internal alignment or embedding of a substring into a target string

Answer 56

local alignment

Question 57

general local alignment method based on dynamic programming

Answer 57

Smith-Waterman algorithm

Question 58

Pairwise sequence alignment methods

Answer 58

brute force alignment dot matrices dynamic programming

Question 59

its objective is to arrange two sequences in such a fashion that pairs of matching characters between the two sequences are maximized

Answer 59

pairwise sequence alignment

Question 60

function that ranks or scores the characters being compared

Answer 60

substitution matrix

Question 61

simplesst case of pairwise sequence

Answer 61

brute force alignments

Question 62

make the brute force method unusable for all but the shortest sequence

Answer 62

gaps

Question 63

pair of related sequences often have insertions or deletions relative to one another, we therefore require

Answer 63

gapped pairwise alignment

Question 64

simple graphical method for pairwise alignment;

Answer 64

dot plot/dot matrix approach

Question 65

no scoring, so difficult to compare alternative alignments

Answer 65

dot plot/dot matrix approach

Question 66

can give visual sequence structure but requires human interaction

Answer 66

dot plot/dot matrix approach

Question 67

provides optimal solutions (but not necessarily unique solutions)

Answer 67

dynamic program algorithm

Question 68

much faster, widely used for database searches, may miss some pairws with low similarity

Answer 68

heuristic word or k-tuple approaches