Course : Bioinformatics

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) Gene Exon In this application, one of the sequences has to be matched entirely (the exon), and the other sequence will be matched partially (the gene). (a) Based on the global sequence alignment algorithm, discuss how the alignment algorithm can be changed to support the Gene-Exon alignment needs. (15 points) (b) Perform semi-global alignment of the two sequences in Question 1(a). Show the dynamic programming table and the directional arrows. What is the optimal alignment and the score? (25 points) 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) Gene Exon In this application, one of the sequences has to be matched entirely (the exon), and the other sequence will be matched partially (the gene). (a) Based on the global sequence alignment algorithm, discuss how the alignment algorithm can be changed to support the Gene-Exon alignment needs. (15 points) (b) Perform semi-global alignment of the two sequences in Question 1(a). Show the dynamic programming table and the directional arrows. What is the optimal alignment and the score? (25 points)