(10 points) Scoring matrices are used to evaluate pairwise alignments produced b
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Question
(10 points) Scoring matrices are used to evaluate pairwise alignments produced by tools like BLAST. For example, the following alignment would have a total score of 8. This score is the sum of symbol-wise scores and gap penalty scores. In the example below a match for an A is worth +4, a match for a D is worth +6, a match for a E is +5 and a match for a F is +6. An alignment for a E to K is worth +1. In the example alignment below, the total symbol-wise score was +32. The gap penalty scores are -10 for the first position in a gap longer than a single position (as called the "gap opening penality") and -1 otherwise. In the example alignment below, the total gap penalty score was -24 Symbol-wise scores +6+6 +1+5+632 Gap penalty scores 10-1-1-1 10-1 = -24 Using a similar approach, generate an alignment score for the following pairwise alignment using the BLOSUM62 scoring matrix (to compute symbol-wise scores) and the same gap penalties as above. You can find the BLOSUM62 scoring matrix onlineExplanation / Answer
Answer:
Using the BLOSUM62 scoring matrix,an alignment SCORE for the following pairwise alignment is :
Hence,symbol-wise SCORE=5+9+4+2+5+3+4+6+4+5+7=54
Gap panelty SCORE=-10-10-1=-21
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