Consider the alignments below of the sequences QNISEKDLLDTENK and QSEKDAADTKEVV

For each alignment, use the BLOSUM-62 matrix (available in your notes) and the gap opening and extension penalties below to calculate a semi-global alignment score. Note: in a semi-global alignment, gaps at the beginning or end of an alignment are not penalized. 1. BLOSUM-62 substitution matrix, Gap Opening Penalty of 10, Gap Extension Penalty of 1. a. Score for alignment 1 = b. Score for alignment 2 = c. Of the two alignments, which alignment is optimal? 2. BLOSUM-62 substitution matrix, Gap Opening Penalty of 1, Gap Extension Penalty of 0.5. a. Score for alignment 1 = b. Score for alignment 2 = c. Of the two alignments, which alignment is optimal?

3. What is the percent identity for (a) Alignment 1 and (b) Alignment 2?

Alignment 1 EMBOSS 001 EMBOSS 001 Alignment 2 EMBOSS 001 EMBOSS 001 1 QNISE KDLLDTENK. 14 l QSEKDAADTKEVV 13 14 l ONISEKDLLDTENK l Q--SEKDAADT KEVV 13 Alignment 1 EMBOSS 001 EMBOSS 001 Alignment 2 EMBOSS 001 EMBOSS 001 1 QNISE KDLLDTENK. 14 l QSEKDAADTKEVV 13 14 l ONISEKDLLDTENK l Q--SEKDAADT KEVV 13