Bioinformatics - Alignment Test Bank Solution Manual Latest Update 2024 (Rated 100%)
Similarity - Answers Resemblance between 2 characters/ sequences
Homology - Answers Two traits are homolgous if derived from the same ancestor
Similarity allows us to assume - Answers Homology
Sequence similarity can be a result of - Answers chance, convergent evolution (organisms not closely
related devloping similar features), or homology (traits derived from a common ancestor)
Similar function doesn't imply _________ - Answers homology
Similar structuers are ________ but not always - Answers likely to have similar function
Similarity between homolgous sequences can be small if? - Answers there is a rapid rate of change, or
the relationship is ancient
Changes can occur vis - Answers substitutions, insertions, duplications, deletions, inversions, transitions
Changes can ________ sequence homology - Answers mask
Sites don't need to be _______ to be homologous - Answers identical
Who created the dot plots method? what does it do? - Answers Gibbs and McIntrye; Makes use of our
ability to make patterns
What does the main diagonal in a dot plot represent? - Answers it tells us regions where two sequences
are identical
What is the issue with the dot plot? - Answers because it only uses 4 nucleotides, alot of noise is
expected; it might be better for use with a amino acid sequence
What is a word and word size? - Answers can be a nucleotide or amino acid, and the length of that word
would be something the user specifies. The algorithim then looks for that length of a word in both
sequences (identical word), in order to generate dot plot (i.e. if the word size was three, one word
would be AAT if it was found in both sequence)
what is the process of making blocks for dot plots - Answers seperate the sequence into the word size
given, then alphabetize them, and compare the identical words between the two sequences to find
matches
what is the point of using a word? - Answers helps clear noise since we only put a dot down when both
sequences have that word
As you increase the word size what happens? - Answers The dot plot is more stringent, so only the main
line will appear if they are identical
,What will the dot plot look like when there is a deletion in sequence 1/insertion in sequence 2 ? -
Answers There will be a middle line, a pause then a line UNDERNEATH it
What will the dot plot look like when there is a deletion in sequence 2/insertion in sequence 1? -
Answers there will be a middle line, a pause then a line ABOVE it
A tandem (repeat of the seqeunce so AABAAB) duplication in sequence #2 will lead to?) - Answers The
sequences will disconnect but overlap where the tandem is with a sequence below the main diagonal
A tandem duplication in sequence #1 will lead to - Answers the sequences will disconnect but overlap
where the tandem is with a sequence above the main diagonal
What is a nontandem repeat - Answers a repeat that is seperated by a few nucleotides from the thing it
is repeating (ex. AABXXXAAB)
What does a non-tandem repeat look like on a graph? - Answers Little segments cut off from the graph
and not in the middle line
In eukaryotes, a deletion or insertion of a sequence is usually a _______ element - Answers Alu element
What does plotting a sequence against itself help us do? (while also playing around with word size) -
Answers Can tell us about how many units make up the protein, and which units came first (as the older
ones will have more mutations and will disappear when we make the word size more stringent)
what does a dark square on a dot plot show? - Answers regions with the same piece repeating over and
over and over again
Dot plots cannot give us reliable alignments, why? - Answers Because they rely too much on visible
information/analysis
How do we find the best alignment? - Answers Have to use a scoring scheme, and find the best score
using that scoring scheme. What the best scoring scheme itself is, is not something known
`How does needleman and wuncsh work? - Answers gives you the best possible alignment using its
scoring scheme; you have to look at what the best was up until that moment, by looking for the max
within the column or row and adding it to the element your considering. Trace back to see how you got
to the highest score
When a column or row is skipped that is gap
is a needleman and wuncsh a global or local alignment? - Answers a global alignment since your trying
to align all of sequence 1 with all of sequence 2
What is the problem with a global alignment? - Answers highly similar sequences might be missed; as
well it would try to force a small sequence to align with the entirety of a large sequence
, What does a smith waterman alignment do? - Answers provides us with a local alignment
What is different about smith waterman compared to the needleman? - Answers Smith waterman does
three things:
- assigns a negative score to gaps and mismatches
- Has a baseline of 0
- The max can be found anywhere within the sequence; also we start at the top right
What do the smith waterman and needleman have in common? - Answers They both give you the best
answer given your scoring scheme
Global alignment - Answers tries to maximize the number of matches for the entire sequence
Local alignment - Answers tries to maximize the number of matches for a substring
What does BLAST use? - Answers a modified local alignment
Global alignment is bad when - Answers trying to align two diverged sequences (ex. it can't align active
sites properly because its trying to align the whole ass sequences
Why is a gap penalty worth more than a substitution penalty - Answers Because of the biological
implications of a gap (i.e. if its not in a factor of three, there is a frame shift )
What are end gaps? - Answers End gaps are the gaps at the end of a sequence
What is the gap penalty score? What do the letters mean? - Answers W= a+b*k
W= the gap penalty
a= cost of creating a gap
b = cost of extending the gap
k = length of the gap
Why should a be larger than b in the gap penalty equation? - Answers Because the cost of creating a gap
is more oofie than extending one; getting a gap is harder
Why is the gap penalty not an exact science? - Answers Because creating a gap can also depend heavily
on where the gap actually is
When using a protein sequence, why should we not do an alignment with the nucleotides? - Answers
Because a gap penalty wouldnt be properly given for a framsehift versus a indel multiple of three
Similarity - Answers Resemblance between 2 characters/ sequences
Homology - Answers Two traits are homolgous if derived from the same ancestor
Similarity allows us to assume - Answers Homology
Sequence similarity can be a result of - Answers chance, convergent evolution (organisms not closely
related devloping similar features), or homology (traits derived from a common ancestor)
Similar function doesn't imply _________ - Answers homology
Similar structuers are ________ but not always - Answers likely to have similar function
Similarity between homolgous sequences can be small if? - Answers there is a rapid rate of change, or
the relationship is ancient
Changes can occur vis - Answers substitutions, insertions, duplications, deletions, inversions, transitions
Changes can ________ sequence homology - Answers mask
Sites don't need to be _______ to be homologous - Answers identical
Who created the dot plots method? what does it do? - Answers Gibbs and McIntrye; Makes use of our
ability to make patterns
What does the main diagonal in a dot plot represent? - Answers it tells us regions where two sequences
are identical
What is the issue with the dot plot? - Answers because it only uses 4 nucleotides, alot of noise is
expected; it might be better for use with a amino acid sequence
What is a word and word size? - Answers can be a nucleotide or amino acid, and the length of that word
would be something the user specifies. The algorithim then looks for that length of a word in both
sequences (identical word), in order to generate dot plot (i.e. if the word size was three, one word
would be AAT if it was found in both sequence)
what is the process of making blocks for dot plots - Answers seperate the sequence into the word size
given, then alphabetize them, and compare the identical words between the two sequences to find
matches
what is the point of using a word? - Answers helps clear noise since we only put a dot down when both
sequences have that word
As you increase the word size what happens? - Answers The dot plot is more stringent, so only the main
line will appear if they are identical
,What will the dot plot look like when there is a deletion in sequence 1/insertion in sequence 2 ? -
Answers There will be a middle line, a pause then a line UNDERNEATH it
What will the dot plot look like when there is a deletion in sequence 2/insertion in sequence 1? -
Answers there will be a middle line, a pause then a line ABOVE it
A tandem (repeat of the seqeunce so AABAAB) duplication in sequence #2 will lead to?) - Answers The
sequences will disconnect but overlap where the tandem is with a sequence below the main diagonal
A tandem duplication in sequence #1 will lead to - Answers the sequences will disconnect but overlap
where the tandem is with a sequence above the main diagonal
What is a nontandem repeat - Answers a repeat that is seperated by a few nucleotides from the thing it
is repeating (ex. AABXXXAAB)
What does a non-tandem repeat look like on a graph? - Answers Little segments cut off from the graph
and not in the middle line
In eukaryotes, a deletion or insertion of a sequence is usually a _______ element - Answers Alu element
What does plotting a sequence against itself help us do? (while also playing around with word size) -
Answers Can tell us about how many units make up the protein, and which units came first (as the older
ones will have more mutations and will disappear when we make the word size more stringent)
what does a dark square on a dot plot show? - Answers regions with the same piece repeating over and
over and over again
Dot plots cannot give us reliable alignments, why? - Answers Because they rely too much on visible
information/analysis
How do we find the best alignment? - Answers Have to use a scoring scheme, and find the best score
using that scoring scheme. What the best scoring scheme itself is, is not something known
`How does needleman and wuncsh work? - Answers gives you the best possible alignment using its
scoring scheme; you have to look at what the best was up until that moment, by looking for the max
within the column or row and adding it to the element your considering. Trace back to see how you got
to the highest score
When a column or row is skipped that is gap
is a needleman and wuncsh a global or local alignment? - Answers a global alignment since your trying
to align all of sequence 1 with all of sequence 2
What is the problem with a global alignment? - Answers highly similar sequences might be missed; as
well it would try to force a small sequence to align with the entirety of a large sequence
, What does a smith waterman alignment do? - Answers provides us with a local alignment
What is different about smith waterman compared to the needleman? - Answers Smith waterman does
three things:
- assigns a negative score to gaps and mismatches
- Has a baseline of 0
- The max can be found anywhere within the sequence; also we start at the top right
What do the smith waterman and needleman have in common? - Answers They both give you the best
answer given your scoring scheme
Global alignment - Answers tries to maximize the number of matches for the entire sequence
Local alignment - Answers tries to maximize the number of matches for a substring
What does BLAST use? - Answers a modified local alignment
Global alignment is bad when - Answers trying to align two diverged sequences (ex. it can't align active
sites properly because its trying to align the whole ass sequences
Why is a gap penalty worth more than a substitution penalty - Answers Because of the biological
implications of a gap (i.e. if its not in a factor of three, there is a frame shift )
What are end gaps? - Answers End gaps are the gaps at the end of a sequence
What is the gap penalty score? What do the letters mean? - Answers W= a+b*k
W= the gap penalty
a= cost of creating a gap
b = cost of extending the gap
k = length of the gap
Why should a be larger than b in the gap penalty equation? - Answers Because the cost of creating a gap
is more oofie than extending one; getting a gap is harder
Why is the gap penalty not an exact science? - Answers Because creating a gap can also depend heavily
on where the gap actually is
When using a protein sequence, why should we not do an alignment with the nucleotides? - Answers
Because a gap penalty wouldnt be properly given for a framsehift versus a indel multiple of three
