The third kind of sequence alignment is called semi-global alignment . It is a modification from the standard global alignment in a way that penalty at the sequence beginning and/or ending are not charged (i.e. no penalty). This can be used in applications such as Gene-Exon alignment (i.e. finding an exon in a gene sequence):

In this application, one of the sequences has to be matched entirely (the exon), and the other sequence will be matched partially (the gene).

Question 1: Based on the global sequence alignment algorithm, discuss how the alignment algorithm can be changed to support the Gene-Exon alignment needs.

Question 2: Perform semi-global alignment of the two sequences given as following. Show the dynamic programming table and the directional arrows. What is the optimal alignment and the score?

X = CAGCACTTGGATTCTCGG

Y = CAGCGTGG