In a simple base-identity dot-plot

 In a simple base-identity dot-plot

6. In a simple base-identity dot-plot, what represents an optimal alignment? (score is 1 if bases i and j are the same, and 0 otherwise)

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Group of answer choices

 

The set of dots that are colored and contiguous, where color denotes score.

 

The graph path along the diagonal with the highest number of ‘1’ elements

 

The graph path with the smallest number of off-diagonal elements scoring ‘1’

 

It is not possible to generalize this; You need an alignment algorithm.

 

7. What does the BLOSUM62 alignment score matrix represent mathematically?

Group of answer choices

 

Acceptability of amino acid substitutions based on aligned “blocks” in proteins with 62% identity or less.

 

An amino acid model for protein evolution that also serves as a scoring matrix for sequence alignments.

 

Scoring model for comparison of protein or nucleotide sequences, for example with BLAST.

 

Commonality of amino acid residues based on aligned peptides with 62% identity.

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