Alice would like to compare two DNA sequences, seq1 (ACCATCGGA) and eq2 (ATCCATG

Question

Alice would like to compare two DNA sequences, seq1 (ACCATCGGA) and eq2 (ATCCATGGGA). She came up with two pairwise alignments, alignmen and alignment Y (shown below). She would like to determine which of these two alignments is more optimal using the associated scoring scheme (below). scoring scheme seql A-CCATCGGA seq2 ATCCATGGGA seq1 ACC-ATCGGA match seq2 ATCCATGGGAmismatch1 gap open3 gap extend = -1 alignment X alignmentY Alice has determined that alignment Y is more optimal than alignment X. Do you agree with Alice? Briefly explain why and show your calculations

Explanation / Answer

Let us calculate total score in both alignment:

For alignment X:

Total number of matches=8

Total number of mismatches=1

Total number of gap open=1

Total number of gap extend=0

So, total score=(3*8)+(1*1)+(-3*1)+(1*0)

=24+1-3

=22

For alignment Y:

Total number of matches=7

Total number of mismatches=2

Total number of gap open=1

Total number of gap extend=0

So, total score=(3*7)+(1*2)+(-3*1)+(1*0)

=21+2-3

=20

As here, score of alignment X >score of alignment Y. So, alignment X is more optimal.

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