Question 1: Part A. Using global alignment and Needleman–Wunsch algorithm, find

Question

Question 1:

Part A.

Using global alignment and Needleman–Wunsch algorithm, find the optimal alignment and calculate the score of aligning the following two sequences using PAM 250

Given: gap extension penalty=-8

Sequences: APVMR & APYPR

Part B.

Obtain the human Hemoglobin subunit alpha and human hemoglobin subunit delta protein sequences from the "RefSeq" database at NCBI "https://www.ncbi.nlm.nih.gov/" and write their accession numbers.

Part C.

For the two sequences in "B", perform pairwise sequence alignment at the NCBI BLAST website "https://blast.ncbi.nlm.nih.gov/Blast.cgi" using PAM250 and BLOSUM90 and record the score, the number of gaps, the percent identity, and the length of the aligned region.

Score Number of gaps Percent identity Length of aligned region PAM250 BLOSUM90

Explanation / Answer

Part A: Score: 13

Part B:

Human haemoglobin cahin A :

Human Haemoglobin chain B

Part C:

score no of gaps % identity length of aligned region PAM250 108 bits 8 43% 99% BLOSUM90 118bits 8 43% 98%

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