Bioinformatics - Align Two Sequences - Assessment Answer

Bioinformatics Assignment

Assignment Task

• 1) How many ways can you align two sequences, each containing two resides, Seq1:AB and Seq2:CD ? (ABC & D are residues found in Seq 1 and Seq 2).

1-a) First when no insertion/deletion are allowed

1-b) Second, when you are allowed to have insertions/deletions.

Write down the number of possible way to align two sequences and then indicate all possible alignments.

2) Please discuss how many ways you can align two sequences, each containing 3 residues, Seq1:ABC and Seq2:XYZ.

2-a) Start with no insertion/deletion anywhere,

2-b) Then insertion/deletion is allowed at the beginning and at the end of the sequence but not in the middle.

2-c) Then insertion//deletion is allowed at any position including in the middle.

Write down the number of possible way to align two sequences and then indicate all possible alignments.

Answer 1- As given first sequence=AB and second sequence=CD, where ABCD are residues in given protein.

(If A=C and B=D means A and C are same residues and B and D are same residues)

• When no insertion and deletion is allowed then number of possible ways to align these sequences can be one and the possible alignment:

A B

C D

• When insertion and deletion are allowed, the number of possible ways, these two sequences can be aligned will be zero.

Answer 2-As given first sequence=ABC and second sequence=XYZ, where A, B, C, X, Y and Z are residues in given protein. (If A=X, B=Y and C=Z)

• When no insertion and deletion are allowed then possible number of alignment=5 with possible alignment

A B C

X Y Z

• The insertion/deletions are allowed at the beginningor at the end of the sequence, and then number of possible alignmentwill be zero
• If insertion and deletion at any position, lets insert a bar at 2^ndposition in 2^ndsequence(XYZ), then number of possible alignmentwill be one

A B C

X D Y Z