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Chapter 2 Topics
Chapter 2 Learning Objective
11
Biology
Undergraduate 4
02/22/2012

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Cards

Term
What is a global sequence alignment?
Definition
finds the best alignment score over the entire sequence
Term
What is a local sequence alignment?
Definition
finds the best alignment score for the longest stretch of residues
Term
What are the three rules of amino acid substitution according to Margaret Dayhoff?
Definition
amino acids wiht an important structural or functional role are less mutable; amino acids with functions that are easily done by other residues are highly mutable; common substitutions only require a single nucleotide change
Term
What matrix would you use if the sequences are less divergent?
Definition
PAM(low) or BLOSUM(high)
Term
What matrix would you use if the sequences are more divergent?
Definition
PAM(high) or BLOSUM(low)
Term
What are properties of rigorous alignment methods?
Definition
optimal alignment, slow queries
Term
Examples of rigorous alignment methods?
Definition
Needleman Wunsch Algorithm; Smith Waterman Algorithm
Term
What are properties of heuristic alignment methods?
Definition
not guarenteed to give an optimal alignment, fast queries
Term
Examples of heuristic alignment methods.
Definition
FASTA; BLAST
Term
Explain the FASTA method.
Definition
Finds runs of identical words in dot matrix; Uses 10 highest scoring alignments to rescore in PAM250; Joins ungapped segments by inserting gaps; uses dynamic programming to align the best scoring sequences
Term
Explain the BLAST method.
Definition
Parses query into 3 letter words; Compare word list to database and identify matches that exceed a threshold; for each match, extend in both directions to find alignments greater than threshold
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