A$.$ The history of bioinformatics begins with the advent of sequence alignment technologies.

Name THREE applications of sequence alignments. $(3$ marks$)$ Which alignment approach

should be used for aligning closely related sequences with roughly equal length? $(2$ marks$)$

Name ONE example algorithm of this alignment approach. $(2$ marks$)$

B$.$ Using the alignment algorithm as mentioned in Question $2$A$,$ align the following two strings:

$$ String $1$: AGGATC

$$ String $2$: ACCG

using the following scoring scheme. Provide the dynamic programming array and mark the

trace back route $(6$ marks$),$ then report the alignment and alignment score $(4$ marks$).$

$$ Match $=1$

$$ Mismatch $=-1$

$$ Gap penalty $=-2$

Hint: There may be multiple possible trace back routes and alignments between the two strings. Just

provide one of them.