BIOL 266 Final Exam
Study online at https://quizlet.com/_furj4c
1. Core data -the key information inputted in the database entry
-minimal information is given to identify the data
2. Annotations all additional information to identify data that may change
over time
3. P AND Q all query searches that include both P and Q, but not
separately
4. P OR Q all query searches that include both P and Q, together or
separately
5. P NOT Q all query searches that include just P, but nothing with Q
6. P NOR Q query searches that do not include P or Q
7. P NAND Q all query searches that include P and Q separately, every-
thing else except for P and Q co-occurring
8. P XOR Q query searches including P and Q occurring separately,
not together
9. P XNOR Q query searches including P and Q together (not separate-
ly), and everything outside
10. global alignment attempting to align an entire sequence
11. local alignment attempting to align stretches of sequence with higher
density of matches
12. What is the - While looking at all alignment possibilities is the best
best algorithm way to determine the best possible alignment, this is not
for determining feasible
the best align- - Dynamic programming is the best algorithm to approxi-
ment between mate the best alignment
two sequences?
13. How does a dy- - break the problem (sequence) into smaller subsets and
namic program- solve them all individually, then put them back together
, BIOL 266 Final Exam
Study online at https://quizlet.com/_furj4c
ming algorithm
work?
14. What scoring -BLOSUM62
matrix is used - is a 20x20 matrix that scores how often certain amino
for proteins, and acids align
how does it - high positive scores indicate that the pairing is rare, and
work? therefore more significant
15. How is scoring -certain base changes are penalized more than others
different within a - transversions (changing from purine to pyrimidine) is pe-
translation/trans- nalized higher than translations (purine/purine or pyrimi-
version matrix? dine/pyrimidine)
16. What type of Global alignment
alignment al-
gorithm is
the Needle-
man-Wunsch?
17. What type of - Local alignment
alignment al- - Scoring is harsher- mismatches are scored as 0, and if
gorithm is a score is negative it is scored as 0 in the matrix
the Smith-Water-
man, and how
does it differ
from the Needle-
man-Wunsch?
18. Homology similarity due to common ancestry
19. What is a flat file A database in which all the data is stored in a single
database? table/file that may be downloaded
20. What is a rela- database where the data is separated into different tables
tional database? so you can easily find what you are looking for
21. Why are oper- databases are very large, and operators help to limit in-
ators useful in formation gathered from a search and specify the results
query searches?
, BIOL 266 Final Exam
Study online at https://quizlet.com/_furj4c
22. What is a heuris- An approximate answer to what the solution likely is
tic approach, and -used when it is not feasible to examine all possible solu-
when is it used? tions (ie too large of a dataset)
23. What is BLAST, -Basic Local Alignment Search Tool
and how does it - heuristic procedure
work? - initially finds ungapped, locally optimal sequence align-
ments and then chops the sequence into smaller frames
-search the database to find sequences that share the
frames, which will be candidates for alignment
- candidates will be aligned with original sequence using
Smith-Waterman algorithm
24. What is an ex- the number of matches with scores equivalent to or better
pectation (E) val- than the sequence that are expected to occur in the
ue? database search
- the smaller the E-value, the less likely it is to find a better
match
25. blastp protein vs protein database
26. blastn nucleotide vs nucleotide database
27. blastx Search protein database using a translated nucleotide
query
28. tblastn search translated nucleotide database using a protein
query
29. tblastx Search translated nucleotide database using a translated
nucleotide query
30. bit score the local alignment score given following a BLAST search
31. Why is it not Genetic relatedness can only be fully determined by using
guaranteed that a phylogenetic tree
the top hit after
a BLAST search
Study online at https://quizlet.com/_furj4c
1. Core data -the key information inputted in the database entry
-minimal information is given to identify the data
2. Annotations all additional information to identify data that may change
over time
3. P AND Q all query searches that include both P and Q, but not
separately
4. P OR Q all query searches that include both P and Q, together or
separately
5. P NOT Q all query searches that include just P, but nothing with Q
6. P NOR Q query searches that do not include P or Q
7. P NAND Q all query searches that include P and Q separately, every-
thing else except for P and Q co-occurring
8. P XOR Q query searches including P and Q occurring separately,
not together
9. P XNOR Q query searches including P and Q together (not separate-
ly), and everything outside
10. global alignment attempting to align an entire sequence
11. local alignment attempting to align stretches of sequence with higher
density of matches
12. What is the - While looking at all alignment possibilities is the best
best algorithm way to determine the best possible alignment, this is not
for determining feasible
the best align- - Dynamic programming is the best algorithm to approxi-
ment between mate the best alignment
two sequences?
13. How does a dy- - break the problem (sequence) into smaller subsets and
namic program- solve them all individually, then put them back together
, BIOL 266 Final Exam
Study online at https://quizlet.com/_furj4c
ming algorithm
work?
14. What scoring -BLOSUM62
matrix is used - is a 20x20 matrix that scores how often certain amino
for proteins, and acids align
how does it - high positive scores indicate that the pairing is rare, and
work? therefore more significant
15. How is scoring -certain base changes are penalized more than others
different within a - transversions (changing from purine to pyrimidine) is pe-
translation/trans- nalized higher than translations (purine/purine or pyrimi-
version matrix? dine/pyrimidine)
16. What type of Global alignment
alignment al-
gorithm is
the Needle-
man-Wunsch?
17. What type of - Local alignment
alignment al- - Scoring is harsher- mismatches are scored as 0, and if
gorithm is a score is negative it is scored as 0 in the matrix
the Smith-Water-
man, and how
does it differ
from the Needle-
man-Wunsch?
18. Homology similarity due to common ancestry
19. What is a flat file A database in which all the data is stored in a single
database? table/file that may be downloaded
20. What is a rela- database where the data is separated into different tables
tional database? so you can easily find what you are looking for
21. Why are oper- databases are very large, and operators help to limit in-
ators useful in formation gathered from a search and specify the results
query searches?
, BIOL 266 Final Exam
Study online at https://quizlet.com/_furj4c
22. What is a heuris- An approximate answer to what the solution likely is
tic approach, and -used when it is not feasible to examine all possible solu-
when is it used? tions (ie too large of a dataset)
23. What is BLAST, -Basic Local Alignment Search Tool
and how does it - heuristic procedure
work? - initially finds ungapped, locally optimal sequence align-
ments and then chops the sequence into smaller frames
-search the database to find sequences that share the
frames, which will be candidates for alignment
- candidates will be aligned with original sequence using
Smith-Waterman algorithm
24. What is an ex- the number of matches with scores equivalent to or better
pectation (E) val- than the sequence that are expected to occur in the
ue? database search
- the smaller the E-value, the less likely it is to find a better
match
25. blastp protein vs protein database
26. blastn nucleotide vs nucleotide database
27. blastx Search protein database using a translated nucleotide
query
28. tblastn search translated nucleotide database using a protein
query
29. tblastx Search translated nucleotide database using a translated
nucleotide query
30. bit score the local alignment score given following a BLAST search
31. Why is it not Genetic relatedness can only be fully determined by using
guaranteed that a phylogenetic tree
the top hit after
a BLAST search
