BIOL 266 Final Exam UPDATED ACTUAL Exam Questions and CORRECT Answers
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Course
BIOL 266
Institution
BIOL 266
BIOL 266 Final Exam UPDATED
ACTUAL Exam Questions and CORRECT
Answers
Core data - CORRECT ANSWER- -the key information inputted in the database entry
-minimal information is given to identify the data
Annotations - CORRECT ANSWER- all additional information to identify data that may
change...
BIOL 266 Final Exam UPDATED
ACTUAL Exam Questions and CORRECT
Answers
Core data - CORRECT ANSWER- ✔✔-the key information inputted in the database entry
-minimal information is given to identify the data
Annotations - CORRECT ANSWER- ✔✔all additional information to identify data that may
change over time
P AND Q - CORRECT ANSWER- ✔✔all query searches that include both P and Q, but not
separately
P OR Q - CORRECT ANSWER- ✔✔all query searches that include both P and Q, together or
separately
P NOT Q - CORRECT ANSWER- ✔✔all query searches that include just P, but nothing with
Q
P NOR Q - CORRECT ANSWER- ✔✔query searches that do not include P or Q
P NAND Q - CORRECT ANSWER- ✔✔all query searches that include P and Q separately,
everything else except for P and Q co-occurring
P XOR Q - CORRECT ANSWER- ✔✔query searches including P and Q occurring
separately, not together
P XNOR Q - CORRECT ANSWER- ✔✔query searches including P and Q together (not
separately), and everything outside
global alignment - CORRECT ANSWER- ✔✔attempting to align an entire sequence
,local alignment - CORRECT ANSWER- ✔✔attempting to align stretches of sequence with
higher density of matches
What is the best algorithm for determining the best alignment between two sequences? -
CORRECT ANSWER- ✔✔- While looking at all alignment possibilities is the best way to
determine the best possible alignment, this is not feasible
- Dynamic programming is the best algorithm to approximate the best alignment
How does a dynamic programming algorithm work? - CORRECT ANSWER- ✔✔- break the
problem (sequence) into smaller subsets and solve them all individually, then put them back
together
What scoring matrix is used for proteins, and how does it work? - CORRECT ANSWER-
✔✔-BLOSUM62
- is a 20x20 matrix that scores how often certain amino acids align
- high positive scores indicate that the pairing is rare, and therefore more significant
How is scoring different within a translation/transversion matrix? - CORRECT ANSWER-
✔✔-certain base changes are penalized more than others
- transversions (changing from purine to pyrimidine) is penalized higher than translations
(purine/purine or pyrimidine/pyrimidine)
What type of alignment algorithm is the Needleman-Wunsch? - CORRECT ANSWER-
✔✔Global alignment
What type of alignment algorithm is the Smith-Waterman, and how does it differ from the
Needleman-Wunsch? - CORRECT ANSWER- ✔✔- Local alignment
- Scoring is harsher- mismatches are scored as 0, and if a score is negative it is scored as 0 in
the matrix
Homology - CORRECT ANSWER- ✔✔similarity due to common ancestry
What is a flat file database? - CORRECT ANSWER- ✔✔A database in which all the data is
stored in a single table/file that may be downloaded
, What is a relational database? - CORRECT ANSWER- ✔✔database where the data is
separated into different tables so you can easily find what you are looking for
Why are operators useful in query searches? - CORRECT ANSWER- ✔✔databases are very
large, and operators help to limit information gathered from a search and specify the results
What is a heuristic approach, and when is it used? - CORRECT ANSWER- ✔✔An
approximate answer to what the solution likely is
-used when it is not feasible to examine all possible solutions (ie too large of a dataset)
What is BLAST, and how does it work? - CORRECT ANSWER- ✔✔-Basic Local Alignment
Search Tool
- heuristic procedure
- initially finds ungapped, locally optimal sequence alignments 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
What is an expectation (E) value? - CORRECT ANSWER- ✔✔the number of matches with
scores equivalent to or better than the sequence that are expected to occur in the database
search
- the smaller the E-value, the less likely it is to find a better match
blastp - CORRECT ANSWER- ✔✔protein vs protein database
blastn - CORRECT ANSWER- ✔✔nucleotide vs nucleotide database
blastx - CORRECT ANSWER- ✔✔Search protein database using a translated nucleotide
query
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