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BIOL 266 Final Exam Study Guide Solutions Core data - ANSWER--the key information inputted in the database entry -minimal information is given to identify the data Annotations - ANSWER-all additional information to identify data that may change over time P AND Q - ANSWER-all query searches that...

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  • November 3, 2024
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  • 2024/2025
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BIOL 266 Final Exam Study Guide Solutions


Core data - ANSWER✔✔--the key information inputted in the database entry


-minimal information is given to identify the data


Annotations - ANSWER✔✔-all additional information to identify data that may change over time


P AND Q - ANSWER✔✔-all query searches that include both P and Q, but not separately


P OR Q - ANSWER✔✔-all query searches that include both P and Q, together or separately


P NOT Q - ANSWER✔✔-all query searches that include just P, but nothing with Q


P NOR Q - ANSWER✔✔-query searches that do not include P or Q


P NAND Q - ANSWER✔✔-all query searches that include P and Q separately, everything else except for P

and Q co-occurring


P XOR Q - ANSWER✔✔-query searches including P and Q occurring separately, not together


P XNOR Q - ANSWER✔✔-query searches including P and Q together (not separately), and everything

outside


global alignment - ANSWER✔✔-attempting to align an entire sequence


local alignment - ANSWER✔✔-attempting to align stretches of sequence with higher density of matches




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What is the best algorithm for determining the best alignment between two sequences? - 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? - 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? - 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? - 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? - ANSWER✔✔-Global alignment


What type of alignment algorithm is the Smith-Waterman, and how does it differ from the Needleman-

Wunsch? - 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 - ANSWER✔✔-similarity due to common ancestry


What is a flat file database? - ANSWER✔✔-A database in which all the data is stored in a single table/file

that may be downloaded

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What is a relational database? - 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? - 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? - 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? - 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? - 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 - ANSWER✔✔-protein vs protein database


blastn - ANSWER✔✔-nucleotide vs nucleotide database


blastx - ANSWER✔✔-Search protein database using a translated nucleotide query



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